############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ISAnalytics ### ############################################################################## ############################################################################## * checking for file ‘ISAnalytics/DESCRIPTION’ ... OK * preparing ‘ISAnalytics’: * checking DESCRIPTION meta-information ... OK * installing the package to process help pages * building the PDF package manual Hmm ... looks like a package Converting Rd files to LaTeX ...... Creating pdf output from LaTeX ... This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode LaTeX2e <2020-02-02> patch level 2 L3 programming layer <2020-02-14> (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 378. 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(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty) (/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/t1zi4.fd) [1{/var/lib/texm f/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) [2] Overfull \hbox (25.5492pt too wide) in paragraph at lines 88--92 \T1/ptm/m/n/10 group. For more de-tails on how to use this func-tion: \T1/zi4/m /n/10 vignette("aggregate_function_usage",package [3] Overfull \hbox (83.22833pt too wide) in paragraph at lines 149--154 \T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun c-tion: \T1/zi4/m/n/10 vignette("aggregate_function_usage",package [4] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [5] Overfull \hbox (87.43779pt too wide) in paragraph at lines 289--291 []\T1/ptm/m/n/10 Either a sin-gle ma-trix or a list of ma-tri-ces, ide-ally ob- tained via \T1/zi4/m/n/10 import_parallel_Vispa2Matrices() [6] [7] Overfull \hbox (7.2896pt too wide) in paragraph at lines 446--450 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_ launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association _file[][][]()\T1/ptm/m/n/10 , [8] [9] Overfull \hbox (21.58893pt too wide) in paragraph at lines 567--570 []\T1/ptm/m/n/10 Additional named ar-gu-ments to pass on to cho-sen de-vice, \T 1/zi4/m/n/10 circlize::circos.par()\T1/ptm/m/n/10 , Overfull \hbox (25.29086pt too wide) in paragraph at lines 567--570 \T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n /10 circlize::circos.genomicLabels() [10] Overfull \hbox (47.36969pt too wide) in paragraph at lines 592--599 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 , Overfull \hbox (92.28088pt too wide) in paragraph at lines 626--633 \T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120 6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] [11] Overfull \hbox (30.68967pt too wide) in paragraph at lines 702--714 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [12] [13] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [14] Overfull \hbox (77.36969pt too wide) in paragraph at lines 850--857 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 HSC_population_ plot[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\ T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n /10 , [15] Overfull \hbox (83.3352pt too wide) in paragraph at lines 923--927 []\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained via [][]im-port_parallel_Vispa2Matrices_interactive[][][] [16] Overfull \hbox (1.63855pt too wide) in paragraph at lines 1008--1011 []\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th e \T1/zi4/m/n/10 mandatory_IS_vars() Overfull \hbox (20.16898pt too wide) in paragraph at lines 1008--1011 \T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4 /m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 ) [17] [18] Overfull \hbox (9.28818pt too wide) in paragraph at lines 1136--1148 \T1/ptm/m/n/10 data frame con-tains the ref-er-ence of pre-recalibration val-ue s for \T1/zi4/m/n/10 chr\T1/ptm/m/n/10 , \T1/zi4/m/n/10 strand \T1/ptm/m/n/10 a nd \T1/zi4/m/n/10 integration_locus [19] [20] Overfull \hbox (50.20969pt too wide) in paragraph at lines 1257--1269 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_is[][][]()\T1/ptm/m/n/10 , Overfull \hbox (40.36096pt too wide) in paragraph at lines 1257--1269 [][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4 /m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [21] Overfull \hbox (95.20969pt too wide) in paragraph at lines 1333--1345 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (40.36096pt too wide) in paragraph at lines 1333--1345 [][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4 /m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [22] Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 []\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/ m/it/10 pa- Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 \T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it /10 , Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 \T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and [23] [24] [25] [26] Overfull \hbox (29.30962pt too wide) in paragraph at lines 1573--1577 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix [][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() [27] Overfull \hbox (19.25786pt too wide) in paragraph at lines 1624--1629 []\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for ex-am-ple c("CLOEXP", "PROJECT1100", Overfull \hbox (59.30962pt too wide) in paragraph at lines 1639--1643 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix [][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() [28] Overfull \hbox (62.36969pt too wide) in paragraph at lines 1691--1698 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 , [29] [30] Overfull \hbox (3.4271pt too wide) in paragraph at lines 1790--1792 []\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match -ing is case-insensitive. Overfull \hbox (2.29784pt too wide) in paragraph at lines 1822--1831 \T1/ptm/m/n/10 orig-i-nal ma-trix are kept if the se-quence count value is grea ter or equal than the \T1/zi4/m/n/10 seqCount_threshold [31] [32] Overfull \hbox (5.10971pt too wide) in paragraph at lines 1909--1912 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . Overfull \hbox (115.40988pt too wide) in paragraph at lines 1933--1937 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][ ][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() [33] Overfull \hbox (5.10971pt too wide) in paragraph at lines 1996--1999 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . Overfull \hbox (25.32918pt too wide) in paragraph at lines 2012--2014 []\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file Overfull \hbox (80.40988pt too wide) in paragraph at lines 2023--2027 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() [34] Overfull \hbox (64.31819pt too wide) in paragraph at lines 2085--2087 []\T1/ptm/m/n/10 For more de-tails see the "How to use im-port func-tions" vi-g nette: \T1/zi4/m/n/10 vignette("import_functions_howto",package [35] Overfull \hbox (100.40988pt too wide) in paragraph at lines 2094--2098 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][][]() Overfull \hbox (3.81735pt too wide) in paragraph at lines 2143--2146 \T1/ptm/m/n/10 el-e-ments rep-re-sent reg-u-lar ex-pres-sions. For de-faults se e [][]de-fault_iss_file_prefixes[][][]. [36] Overfull \hbox (5.10971pt too wide) in paragraph at lines 2155--2158 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . [37] [38] Overfull \hbox (32.36969pt too wide) in paragraph at lines 2274--2281 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [39] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2396--2408 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (55.36096pt too wide) in paragraph at lines 2396--2408 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_ sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [40] [41] Overfull \hbox (122.32698pt too wide) in paragraph at lines 2500--2505 []\T1/ptm/m/n/10 The func-tion ac-cepts mul-ti-ple in-puts for dif-fer-ent sce- nar-ios, please re-fer to the vi-gnette \T1/zi4/m/n/10 vignette("sharing_analys es",package [42] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2528--2540 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (55.36096pt too wide) in paragraph at lines 2528--2540 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss _source[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [43] Overfull \hbox (51.20859pt too wide) in paragraph at lines 2611--2613 []\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2 Matrices_auto\T1/ptm/m/n/10 . [44] [45] Overfull \hbox (5.10971pt too wide) in paragraph at lines 2716--2719 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . [46] [47] [48] [49] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2973--2985 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (40.36096pt too wide) in paragraph at lines 2973--2985 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_ sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4 /m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , Overfull \hbox (118.70859pt too wide) in paragraph at lines 3008--3012 []\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel _vispa2Matrices_interactive [50] Overfull \hbox (16.08829pt too wide) in paragraph at lines 3057--3064 \T1/ptm/m/n/10 rea-son you re-moved the col-li-sions by pass-ing only the se-qu ence count ma-trix to \T1/zi4/m/n/10 remove_collisions()\T1/ptm/m/n/10 , Overfull \hbox (25.75836pt too wide) in paragraph at lines 3074--3076 []\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio ns via \T1/zi4/m/n/10 remove_collisions() Overfull \hbox (33.86833pt too wide) in paragraph at lines 3084--3086 []\T1/ptm/m/n/10 For more de-tails on how to use col-li-sion re-moval func-tion -al-ity: \T1/zi4/m/n/10 vignette("collision_removal",package [51] [52] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [53] Overfull \hbox (19.7378pt too wide) in paragraph at lines 3226--3236 \T1/ptm/m/n/10 tails re-fer to the vi-gnette "Col-li-sion re-moval func-tion-al -ity": \T1/zi4/m/n/10 vignette("collision_removal",package [54] Overfull \hbox (33.6188pt too wide) in paragraph at lines 3260--3262 []\T1/ptm/m/n/10 The date col-umn that should be con-sid-ered. Must be one valu e in \T1/zi4/m/n/10 date_columns_coll() Overfull \hbox (5.10971pt too wide) in paragraph at lines 3271--3274 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . [55] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3376--3388 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (20.36096pt too wide) in paragraph at lines 3376--3388 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_ sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [56] [57] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3458--3470 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [58] Overfull \hbox (32.36969pt too wide) in paragraph at lines 3542--3549 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [59] Overfull \hbox (32.36969pt too wide) in paragraph at lines 3617--3624 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [60] Overfull \hbox (3.36687pt too wide) in paragraph at lines 3677--3683 \T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 . Overfull \hbox (14.32507pt too wide) in paragraph at lines 3677--3683 \T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com parators [61] [62] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3848--3860 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [63] [64] Overfull \hbox (32.36969pt too wide) in paragraph at lines 3964--3971 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [65] Overfull \hbox (12.649pt too wide) in paragraph at lines 4000--4002 []\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns Overfull \hbox (95.20969pt too wide) in paragraph at lines 4047--4059 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [66] Overfull \hbox (99.30962pt too wide) in paragraph at lines 4114--4118 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix [][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]() [67] No file Rd2.ind. [68] (/tmp/RtmpR4QPxb/Rbuild13fdf567ab114b/ISAnalytics/.Rd2pdf1310197/Rd2.aux) Package rerunfilecheck Warning: File `Rd2.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.dynamic.Rdash.dots} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glue} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.auto } has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.inte ractive} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us r/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texm f-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc} Output written on Rd2.pdf (68 pages, 215572 bytes). Transcript written on Rd2.log. This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode LaTeX2e <2020-02-02> patch level 2 L3 programming layer <2020-02-14> (./Rd2.tex (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2019/12/20 v1.4l Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/home/biocbuild/bbs-3.14-bioc/R/share/texmf/tex/latex/Rd.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/bm.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/times.sty) (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/zi4.sty `inconsolata-zi4' v1.12, 2019/05/17 Text macros for Inconsolata (msharpe) (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/keyval.tex))))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/pdftexcmds/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty)) (/usr/share/texlive/texmf-dist/tex/generic/kvsetkeys/kvsetkeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/kvdefinekeys/kvdefinekeys.sty) (/usr/share/texlive/texmf-dist/tex/generic/pdfescape/pdfescape.sty) (/usr/share/texlive/texmf-dist/tex/latex/hycolor/hycolor.sty) (/usr/share/texlive/texmf-dist/tex/latex/letltxmacro/letltxmacro.sty) (/usr/share/texlive/texmf-dist/tex/latex/auxhook/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/kvoptions/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/generic/intcalc/intcalc.sty) (/usr/share/texlive/texmf-dist/tex/generic/etexcmds/etexcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/bitset/bitset.sty (/usr/share/texlive/texmf-dist/tex/generic/bigintcalc/bigintcalc.sty)) (/usr/share/texlive/texmf-dist/tex/generic/atbegshi/atbegshi.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/atveryend/atveryend.sty) (/usr/share/texlive/texmf-dist/tex/latex/rerunfilecheck/rerunfilecheck.sty (/usr/share/texlive/texmf-dist/tex/generic/uniquecounter/uniquecounter.sty))) Package hyperref Warning: Option `hyperindex' has already been used, (hyperref) setting the option has no effect on input line 378. 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For more de-tails on how to use this func-tion: \T1/zi4/m /n/10 vignette("aggregate_function_usage",package [4] Overfull \hbox (83.22833pt too wide) in paragraph at lines 149--154 \T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun c-tion: \T1/zi4/m/n/10 vignette("aggregate_function_usage",package [5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6] Overfull \hbox (87.43779pt too wide) in paragraph at lines 289--291 []\T1/ptm/m/n/10 Either a sin-gle ma-trix or a list of ma-tri-ces, ide-ally ob- tained via \T1/zi4/m/n/10 import_parallel_Vispa2Matrices() [7] [8] Overfull \hbox (7.2896pt too wide) in paragraph at lines 446--450 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_ launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association _file[][][]()\T1/ptm/m/n/10 , [9] [10] Overfull \hbox (21.58893pt too wide) in paragraph at lines 567--570 []\T1/ptm/m/n/10 Additional named ar-gu-ments to pass on to cho-sen de-vice, \T 1/zi4/m/n/10 circlize::circos.par()\T1/ptm/m/n/10 , Overfull \hbox (25.29086pt too wide) in paragraph at lines 567--570 \T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n /10 circlize::circos.genomicLabels() [11] Overfull \hbox (47.36969pt too wide) in paragraph at lines 592--599 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 , Overfull \hbox (92.28088pt too wide) in paragraph at lines 626--633 \T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120 6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] [12] Overfull \hbox (30.68967pt too wide) in paragraph at lines 702--714 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [13] [14] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [15] Overfull \hbox (77.36969pt too wide) in paragraph at lines 850--857 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 HSC_population_ plot[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\ T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n /10 , [16] Overfull \hbox (83.3352pt too wide) in paragraph at lines 923--927 []\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained via [][]im-port_parallel_Vispa2Matrices_interactive[][][] [17] Overfull \hbox (1.63855pt too wide) in paragraph at lines 1008--1011 []\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th e \T1/zi4/m/n/10 mandatory_IS_vars() Overfull \hbox (20.16898pt too wide) in paragraph at lines 1008--1011 \T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4 /m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 ) [18] [19] Overfull \hbox (9.28818pt too wide) in paragraph at lines 1136--1148 \T1/ptm/m/n/10 data frame con-tains the ref-er-ence of pre-recalibration val-ue s for \T1/zi4/m/n/10 chr\T1/ptm/m/n/10 , \T1/zi4/m/n/10 strand \T1/ptm/m/n/10 a nd \T1/zi4/m/n/10 integration_locus [20] [21] Overfull \hbox (50.20969pt too wide) in paragraph at lines 1257--1269 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_is[][][]()\T1/ptm/m/n/10 , Overfull \hbox (40.36096pt too wide) in paragraph at lines 1257--1269 [][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4 /m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [22] Overfull \hbox (95.20969pt too wide) in paragraph at lines 1333--1345 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (40.36096pt too wide) in paragraph at lines 1333--1345 [][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4 /m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [23] Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 []\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/ m/it/10 pa- Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 \T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it /10 , Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 \T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and [24] [25] [26] [27] Overfull \hbox (29.30962pt too wide) in paragraph at lines 1573--1577 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix [][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() [28] Overfull \hbox (19.25786pt too wide) in paragraph at lines 1624--1629 []\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for ex-am-ple c("CLOEXP", "PROJECT1100", Overfull \hbox (59.30962pt too wide) in paragraph at lines 1639--1643 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix [][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() [29] Overfull \hbox (62.36969pt too wide) in paragraph at lines 1691--1698 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 , [30] [31] Overfull \hbox (3.4271pt too wide) in paragraph at lines 1790--1792 []\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match -ing is case-insensitive. Overfull \hbox (2.29784pt too wide) in paragraph at lines 1822--1831 \T1/ptm/m/n/10 orig-i-nal ma-trix are kept if the se-quence count value is grea ter or equal than the \T1/zi4/m/n/10 seqCount_threshold [32] [33] Overfull \hbox (5.10971pt too wide) in paragraph at lines 1909--1912 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . Overfull \hbox (115.40988pt too wide) in paragraph at lines 1933--1937 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][ ][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() [34] Overfull \hbox (5.10971pt too wide) in paragraph at lines 1996--1999 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . Overfull \hbox (25.32918pt too wide) in paragraph at lines 2012--2014 []\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file Overfull \hbox (80.40988pt too wide) in paragraph at lines 2023--2027 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() [35] Overfull \hbox (64.31819pt too wide) in paragraph at lines 2085--2087 []\T1/ptm/m/n/10 For more de-tails see the "How to use im-port func-tions" vi-g nette: \T1/zi4/m/n/10 vignette("import_functions_howto",package [36] Overfull \hbox (100.40988pt too wide) in paragraph at lines 2094--2098 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][][]() Overfull \hbox (3.81735pt too wide) in paragraph at lines 2143--2146 \T1/ptm/m/n/10 el-e-ments rep-re-sent reg-u-lar ex-pres-sions. For de-faults se e [][]de-fault_iss_file_prefixes[][][]. [37] Overfull \hbox (5.10971pt too wide) in paragraph at lines 2155--2158 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . [38] [39] Overfull \hbox (32.36969pt too wide) in paragraph at lines 2274--2281 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [40] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2396--2408 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (55.36096pt too wide) in paragraph at lines 2396--2408 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_ sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [41] [42] Overfull \hbox (122.32698pt too wide) in paragraph at lines 2500--2505 []\T1/ptm/m/n/10 The func-tion ac-cepts mul-ti-ple in-puts for dif-fer-ent sce- nar-ios, please re-fer to the vi-gnette \T1/zi4/m/n/10 vignette("sharing_analys es",package [43] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2528--2540 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (55.36096pt too wide) in paragraph at lines 2528--2540 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss _source[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [44] Overfull \hbox (51.20859pt too wide) in paragraph at lines 2611--2613 []\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2 Matrices_auto\T1/ptm/m/n/10 . [45] [46] Overfull \hbox (5.10971pt too wide) in paragraph at lines 2716--2719 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . [47] [48] [49] [50] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2973--2985 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (40.36096pt too wide) in paragraph at lines 2973--2985 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_ sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4 /m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , Overfull \hbox (118.70859pt too wide) in paragraph at lines 3008--3012 []\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel _vispa2Matrices_interactive [51] Overfull \hbox (16.08829pt too wide) in paragraph at lines 3057--3064 \T1/ptm/m/n/10 rea-son you re-moved the col-li-sions by pass-ing only the se-qu ence count ma-trix to \T1/zi4/m/n/10 remove_collisions()\T1/ptm/m/n/10 , Overfull \hbox (25.75836pt too wide) in paragraph at lines 3074--3076 []\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio ns via \T1/zi4/m/n/10 remove_collisions() Overfull \hbox (33.86833pt too wide) in paragraph at lines 3084--3086 []\T1/ptm/m/n/10 For more de-tails on how to use col-li-sion re-moval func-tion -al-ity: \T1/zi4/m/n/10 vignette("collision_removal",package [52] [53] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [54] Overfull \hbox (19.7378pt too wide) in paragraph at lines 3226--3236 \T1/ptm/m/n/10 tails re-fer to the vi-gnette "Col-li-sion re-moval func-tion-al -ity": \T1/zi4/m/n/10 vignette("collision_removal",package [55] Overfull \hbox (33.6188pt too wide) in paragraph at lines 3260--3262 []\T1/ptm/m/n/10 The date col-umn that should be con-sid-ered. Must be one valu e in \T1/zi4/m/n/10 date_columns_coll() Overfull \hbox (5.10971pt too wide) in paragraph at lines 3271--3274 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . [56] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3376--3388 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (20.36096pt too wide) in paragraph at lines 3376--3388 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_ sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [57] [58] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3458--3470 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [59] Overfull \hbox (32.36969pt too wide) in paragraph at lines 3542--3549 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [60] Overfull \hbox (32.36969pt too wide) in paragraph at lines 3617--3624 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [61] Overfull \hbox (3.36687pt too wide) in paragraph at lines 3677--3683 \T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 . Overfull \hbox (14.32507pt too wide) in paragraph at lines 3677--3683 \T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com parators [62] [63] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3848--3860 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [64] [65] Overfull \hbox (32.36969pt too wide) in paragraph at lines 3964--3971 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [66] Overfull \hbox (12.649pt too wide) in paragraph at lines 4000--4002 []\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns Overfull \hbox (95.20969pt too wide) in paragraph at lines 4047--4059 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [67] Overfull \hbox (99.30962pt too wide) in paragraph at lines 4114--4118 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix [][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]() [68] No file Rd2.ind. [69] (/tmp/RtmpR4QPxb/Rbuild13fdf567ab114b/ISAnalytics/.Rd2pdf1310197/Rd2.aux) ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.dynamic.Rdash.dots} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glue} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.auto } has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.inte ractive} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us r/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texm f-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc} Output written on Rd2.pdf (69 pages, 222374 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (374 entries accepted, 1 rejected). Sorting entries......done (3393 comparisons). Generating output file Rd2.ind....done (379 lines written, 7 warnings). Output written in Rd2.ind. Transcript written in Rd2.ilg. 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For more de-tails on how to use this func-tion: \T1/zi4/m /n/10 vignette("aggregate_function_usage",package [4] Overfull \hbox (83.22833pt too wide) in paragraph at lines 149--154 \T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun c-tion: \T1/zi4/m/n/10 vignette("aggregate_function_usage",package [5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6] Overfull \hbox (87.43779pt too wide) in paragraph at lines 289--291 []\T1/ptm/m/n/10 Either a sin-gle ma-trix or a list of ma-tri-ces, ide-ally ob- tained via \T1/zi4/m/n/10 import_parallel_Vispa2Matrices() [7] [8] Overfull \hbox (7.2896pt too wide) in paragraph at lines 446--450 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_ launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association _file[][][]()\T1/ptm/m/n/10 , [9] [10] Overfull \hbox (21.58893pt too wide) in paragraph at lines 567--570 []\T1/ptm/m/n/10 Additional named ar-gu-ments to pass on to cho-sen de-vice, \T 1/zi4/m/n/10 circlize::circos.par()\T1/ptm/m/n/10 , Overfull \hbox (25.29086pt too wide) in paragraph at lines 567--570 \T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n /10 circlize::circos.genomicLabels() [11] Overfull \hbox (47.36969pt too wide) in paragraph at lines 592--599 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 , Overfull \hbox (92.28088pt too wide) in paragraph at lines 626--633 \T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120 6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] [12] Overfull \hbox (30.68967pt too wide) in paragraph at lines 702--714 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [13] [14] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [15] Overfull \hbox (77.36969pt too wide) in paragraph at lines 850--857 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 HSC_population_ plot[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\ T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n /10 , [16] Overfull \hbox (83.3352pt too wide) in paragraph at lines 923--927 []\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained via [][]im-port_parallel_Vispa2Matrices_interactive[][][] [17] Overfull \hbox (1.63855pt too wide) in paragraph at lines 1008--1011 []\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th e \T1/zi4/m/n/10 mandatory_IS_vars() Overfull \hbox (20.16898pt too wide) in paragraph at lines 1008--1011 \T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4 /m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 ) [18] [19] Overfull \hbox (9.28818pt too wide) in paragraph at lines 1136--1148 \T1/ptm/m/n/10 data frame con-tains the ref-er-ence of pre-recalibration val-ue s for \T1/zi4/m/n/10 chr\T1/ptm/m/n/10 , \T1/zi4/m/n/10 strand \T1/ptm/m/n/10 a nd \T1/zi4/m/n/10 integration_locus [20] [21] Overfull \hbox (50.20969pt too wide) in paragraph at lines 1257--1269 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_is[][][]()\T1/ptm/m/n/10 , Overfull \hbox (40.36096pt too wide) in paragraph at lines 1257--1269 [][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4 /m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [22] Overfull \hbox (95.20969pt too wide) in paragraph at lines 1333--1345 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (40.36096pt too wide) in paragraph at lines 1333--1345 [][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4 /m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [23] Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 []\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/ m/it/10 pa- Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 \T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it /10 , Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 \T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and [24] [25] [26] [27] Overfull \hbox (29.30962pt too wide) in paragraph at lines 1573--1577 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix [][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() [28] Overfull \hbox (19.25786pt too wide) in paragraph at lines 1624--1629 []\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for ex-am-ple c("CLOEXP", "PROJECT1100", Overfull \hbox (59.30962pt too wide) in paragraph at lines 1639--1643 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix [][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() [29] Overfull \hbox (62.36969pt too wide) in paragraph at lines 1691--1698 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 , [30] [31] Overfull \hbox (3.4271pt too wide) in paragraph at lines 1790--1792 []\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match -ing is case-insensitive. Overfull \hbox (2.29784pt too wide) in paragraph at lines 1822--1831 \T1/ptm/m/n/10 orig-i-nal ma-trix are kept if the se-quence count value is grea ter or equal than the \T1/zi4/m/n/10 seqCount_threshold [32] [33] Overfull \hbox (5.10971pt too wide) in paragraph at lines 1909--1912 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . Overfull \hbox (115.40988pt too wide) in paragraph at lines 1933--1937 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][ ][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() [34] Overfull \hbox (5.10971pt too wide) in paragraph at lines 1996--1999 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . Overfull \hbox (25.32918pt too wide) in paragraph at lines 2012--2014 []\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file Overfull \hbox (80.40988pt too wide) in paragraph at lines 2023--2027 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() [35] Overfull \hbox (64.31819pt too wide) in paragraph at lines 2085--2087 []\T1/ptm/m/n/10 For more de-tails see the "How to use im-port func-tions" vi-g nette: \T1/zi4/m/n/10 vignette("import_functions_howto",package [36] Overfull \hbox (100.40988pt too wide) in paragraph at lines 2094--2098 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][][]() Overfull \hbox (3.81735pt too wide) in paragraph at lines 2143--2146 \T1/ptm/m/n/10 el-e-ments rep-re-sent reg-u-lar ex-pres-sions. For de-faults se e [][]de-fault_iss_file_prefixes[][][]. [37] Overfull \hbox (5.10971pt too wide) in paragraph at lines 2155--2158 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . [38] [39] Overfull \hbox (32.36969pt too wide) in paragraph at lines 2274--2281 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [40] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2396--2408 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (55.36096pt too wide) in paragraph at lines 2396--2408 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_ sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [41] [42] Overfull \hbox (122.32698pt too wide) in paragraph at lines 2500--2505 []\T1/ptm/m/n/10 The func-tion ac-cepts mul-ti-ple in-puts for dif-fer-ent sce- nar-ios, please re-fer to the vi-gnette \T1/zi4/m/n/10 vignette("sharing_analys es",package [43] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2528--2540 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (55.36096pt too wide) in paragraph at lines 2528--2540 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss _source[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [44] Overfull \hbox (51.20859pt too wide) in paragraph at lines 2611--2613 []\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2 Matrices_auto\T1/ptm/m/n/10 . [45] [46] Overfull \hbox (5.10971pt too wide) in paragraph at lines 2716--2719 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . [47] [48] [49] [50] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2973--2985 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (40.36096pt too wide) in paragraph at lines 2973--2985 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_ sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4 /m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , Overfull \hbox (118.70859pt too wide) in paragraph at lines 3008--3012 []\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel _vispa2Matrices_interactive [51] Overfull \hbox (16.08829pt too wide) in paragraph at lines 3057--3064 \T1/ptm/m/n/10 rea-son you re-moved the col-li-sions by pass-ing only the se-qu ence count ma-trix to \T1/zi4/m/n/10 remove_collisions()\T1/ptm/m/n/10 , Overfull \hbox (25.75836pt too wide) in paragraph at lines 3074--3076 []\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio ns via \T1/zi4/m/n/10 remove_collisions() Overfull \hbox (33.86833pt too wide) in paragraph at lines 3084--3086 []\T1/ptm/m/n/10 For more de-tails on how to use col-li-sion re-moval func-tion -al-ity: \T1/zi4/m/n/10 vignette("collision_removal",package [52] [53] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [54] Overfull \hbox (19.7378pt too wide) in paragraph at lines 3226--3236 \T1/ptm/m/n/10 tails re-fer to the vi-gnette "Col-li-sion re-moval func-tion-al -ity": \T1/zi4/m/n/10 vignette("collision_removal",package [55] Overfull \hbox (33.6188pt too wide) in paragraph at lines 3260--3262 []\T1/ptm/m/n/10 The date col-umn that should be con-sid-ered. Must be one valu e in \T1/zi4/m/n/10 date_columns_coll() Overfull \hbox (5.10971pt too wide) in paragraph at lines 3271--3274 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . [56] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3376--3388 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (20.36096pt too wide) in paragraph at lines 3376--3388 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_ sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [57] [58] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3458--3470 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [59] Overfull \hbox (32.36969pt too wide) in paragraph at lines 3542--3549 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [60] Overfull \hbox (32.36969pt too wide) in paragraph at lines 3617--3624 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [61] Overfull \hbox (3.36687pt too wide) in paragraph at lines 3677--3683 \T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 . Overfull \hbox (14.32507pt too wide) in paragraph at lines 3677--3683 \T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com parators [62] [63] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3848--3860 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [64] [65] Overfull \hbox (32.36969pt too wide) in paragraph at lines 3964--3971 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [66] Overfull \hbox (12.649pt too wide) in paragraph at lines 4000--4002 []\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns Overfull \hbox (95.20969pt too wide) in paragraph at lines 4047--4059 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [67] Overfull \hbox (99.30962pt too wide) in paragraph at lines 4114--4118 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix [][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]() [68] (/tmp/RtmpR4QPxb/Rbuild13fdf567ab114b/ISAnalytics/.Rd2pdf1310197/Rd2.ind [69] Overfull \hbox (3.3567pt too wide) in paragraph at lines 43--45 []| \T1/zi4/m/n/10 clinical_relevant_suspicious_genes\T1/ptm/m/n/10 , [70] Overfull \hbox (23.3567pt too wide) in paragraph at lines 219--222 []\T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 , LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 302. [71]) (/tmp/RtmpR4QPxb/Rbuild13fdf567ab114b/ISAnalytics/.Rd2pdf1310197/Rd2.aux) Package rerunfilecheck Warning: File `Rd2.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.dynamic.Rdash.dots} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glue} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.auto } has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.inte ractive} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us r/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texm f-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc} Output written on Rd2.pdf (71 pages, 245210 bytes). Transcript written on Rd2.log. This is makeindex, version 2.15 [TeX Live 2019] (kpathsea + Thai support). Scanning input file Rd2.idx....done (374 entries accepted, 1 rejected). Sorting entries......done (3393 comparisons). Generating output file Rd2.ind....done (379 lines written, 7 warnings). Output written in Rd2.ind. Transcript written in Rd2.ilg. 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For more de-tails on how to use this func-tion: \T1/zi4/m /n/10 vignette("aggregate_function_usage",package [4] Overfull \hbox (83.22833pt too wide) in paragraph at lines 149--154 \T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun c-tion: \T1/zi4/m/n/10 vignette("aggregate_function_usage",package [5] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [6] Overfull \hbox (87.43779pt too wide) in paragraph at lines 289--291 []\T1/ptm/m/n/10 Either a sin-gle ma-trix or a list of ma-tri-ces, ide-ally ob- tained via \T1/zi4/m/n/10 import_parallel_Vispa2Matrices() [7] [8] Overfull \hbox (7.2896pt too wide) in paragraph at lines 446--450 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_ launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association _file[][][]()\T1/ptm/m/n/10 , [9] [10] Overfull \hbox (21.58893pt too wide) in paragraph at lines 567--570 []\T1/ptm/m/n/10 Additional named ar-gu-ments to pass on to cho-sen de-vice, \T 1/zi4/m/n/10 circlize::circos.par()\T1/ptm/m/n/10 , Overfull \hbox (25.29086pt too wide) in paragraph at lines 567--570 \T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n /10 circlize::circos.genomicLabels() [11] Overfull \hbox (47.36969pt too wide) in paragraph at lines 592--599 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 , Overfull \hbox (92.28088pt too wide) in paragraph at lines 626--633 \T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120 6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] [12] Overfull \hbox (30.68967pt too wide) in paragraph at lines 702--714 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [13] [14] (/usr/share/texlive/texmf-dist/tex/latex/inconsolata/ts1zi4.fd) [15] Overfull \hbox (77.36969pt too wide) in paragraph at lines 850--857 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 HSC_population_ plot[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\ T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n /10 , [16] Overfull \hbox (83.3352pt too wide) in paragraph at lines 923--927 []\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained via [][]im-port_parallel_Vispa2Matrices_interactive[][][] [17] Overfull \hbox (1.63855pt too wide) in paragraph at lines 1008--1011 []\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th e \T1/zi4/m/n/10 mandatory_IS_vars() Overfull \hbox (20.16898pt too wide) in paragraph at lines 1008--1011 \T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4 /m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 ) [18] [19] Overfull \hbox (9.28818pt too wide) in paragraph at lines 1136--1148 \T1/ptm/m/n/10 data frame con-tains the ref-er-ence of pre-recalibration val-ue s for \T1/zi4/m/n/10 chr\T1/ptm/m/n/10 , \T1/zi4/m/n/10 strand \T1/ptm/m/n/10 a nd \T1/zi4/m/n/10 integration_locus [20] [21] Overfull \hbox (50.20969pt too wide) in paragraph at lines 1257--1269 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_is[][][]()\T1/ptm/m/n/10 , Overfull \hbox (40.36096pt too wide) in paragraph at lines 1257--1269 [][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4 /m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [22] Overfull \hbox (95.20969pt too wide) in paragraph at lines 1333--1345 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (40.36096pt too wide) in paragraph at lines 1333--1345 [][]\T1/zi4/m/n/10 is_sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_so urce[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4 /m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [23] Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 []\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/ m/it/10 pa- Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 \T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it /10 , Underfull \hbox (badness 10000) in paragraph at lines 1388--1388 \T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and [24] [25] [26] [27] Overfull \hbox (29.30962pt too wide) in paragraph at lines 1573--1577 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix [][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() [28] Overfull \hbox (19.25786pt too wide) in paragraph at lines 1624--1629 []\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for ex-am-ple c("CLOEXP", "PROJECT1100", Overfull \hbox (59.30962pt too wide) in paragraph at lines 1639--1643 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix [][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]() [29] Overfull \hbox (62.36969pt too wide) in paragraph at lines 1691--1698 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ ptm/m/n/10 , [][]\T1/zi4/m/n/10 integration_alluvial_plot[][][]()\T1/ptm/m/n/10 , [30] [31] Overfull \hbox (3.4271pt too wide) in paragraph at lines 1790--1792 []\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match -ing is case-insensitive. Overfull \hbox (2.29784pt too wide) in paragraph at lines 1822--1831 \T1/ptm/m/n/10 orig-i-nal ma-trix are kept if the se-quence count value is grea ter or equal than the \T1/zi4/m/n/10 seqCount_threshold [32] [33] Overfull \hbox (5.10971pt too wide) in paragraph at lines 1909--1912 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . Overfull \hbox (115.40988pt too wide) in paragraph at lines 1933--1937 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][ ][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() [34] Overfull \hbox (5.10971pt too wide) in paragraph at lines 1996--1999 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . Overfull \hbox (25.32918pt too wide) in paragraph at lines 2012--2014 []\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file Overfull \hbox (80.40988pt too wide) in paragraph at lines 2023--2027 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_single_Vispa2Matrix[][][]() [35] Overfull \hbox (64.31819pt too wide) in paragraph at lines 2085--2087 []\T1/ptm/m/n/10 For more de-tails see the "How to use im-port func-tions" vi-g nette: \T1/zi4/m/n/10 vignette("import_functions_howto",package [36] Overfull \hbox (100.40988pt too wide) in paragraph at lines 2094--2098 []\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_Vispa2_sta ts[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_association_file[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices[][][]() Overfull \hbox (3.81735pt too wide) in paragraph at lines 2143--2146 \T1/ptm/m/n/10 el-e-ments rep-re-sent reg-u-lar ex-pres-sions. For de-faults se e [][]de-fault_iss_file_prefixes[][][]. [37] Overfull \hbox (5.10971pt too wide) in paragraph at lines 2155--2158 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . [38] [39] Overfull \hbox (32.36969pt too wide) in paragraph at lines 2274--2281 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [40] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2396--2408 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (55.36096pt too wide) in paragraph at lines 2396--2408 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_ sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [41] [42] Overfull \hbox (122.32698pt too wide) in paragraph at lines 2500--2505 []\T1/ptm/m/n/10 The func-tion ac-cepts mul-ti-ple in-puts for dif-fer-ent sce- nar-ios, please re-fer to the vi-gnette \T1/zi4/m/n/10 vignette("sharing_analys es",package [43] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2528--2540 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (55.36096pt too wide) in paragraph at lines 2528--2540 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss _source[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/ zi4/m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [44] Overfull \hbox (51.20859pt too wide) in paragraph at lines 2611--2613 []\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2 Matrices_auto\T1/ptm/m/n/10 . [45] [46] Overfull \hbox (5.10971pt too wide) in paragraph at lines 2716--2719 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . [47] [48] [49] [50] Overfull \hbox (95.20969pt too wide) in paragraph at lines 2973--2985 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (40.36096pt too wide) in paragraph at lines 2973--2985 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_ sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4 /m/n/10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , Overfull \hbox (118.70859pt too wide) in paragraph at lines 3008--3012 []\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel _vispa2Matrices_interactive [51] Overfull \hbox (16.08829pt too wide) in paragraph at lines 3057--3064 \T1/ptm/m/n/10 rea-son you re-moved the col-li-sions by pass-ing only the se-qu ence count ma-trix to \T1/zi4/m/n/10 remove_collisions()\T1/ptm/m/n/10 , Overfull \hbox (25.75836pt too wide) in paragraph at lines 3074--3076 []\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio ns via \T1/zi4/m/n/10 remove_collisions() Overfull \hbox (33.86833pt too wide) in paragraph at lines 3084--3086 []\T1/ptm/m/n/10 For more de-tails on how to use col-li-sion re-moval func-tion -al-ity: \T1/zi4/m/n/10 vignette("collision_removal",package [52] [53] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [54] Overfull \hbox (19.7378pt too wide) in paragraph at lines 3226--3236 \T1/ptm/m/n/10 tails re-fer to the vi-gnette "Col-li-sion re-moval func-tion-al -ity": \T1/zi4/m/n/10 vignette("collision_removal",package [55] Overfull \hbox (33.6188pt too wide) in paragraph at lines 3260--3262 []\T1/ptm/m/n/10 The date col-umn that should be con-sid-ered. Must be one valu e in \T1/zi4/m/n/10 date_columns_coll() Overfull \hbox (5.10971pt too wide) in paragraph at lines 3271--3274 \T1/ptm/m/n/10 no re-port should be pro-duced. De-faults to \T1/zi4/m/n/10 {use r_home}/ISAnalytics_reports\T1/ptm/m/n/10 . [56] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3376--3388 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , Overfull \hbox (20.36096pt too wide) in paragraph at lines 3376--3388 [][]\T1/zi4/m/n/10 cumulative_is[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 is_ sharing[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 iss_source[][][]()\T1/ptm/m/ n/10 , [][]\T1/zi4/m/n/10 purity_filter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [57] [58] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3458--3470 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [59] Overfull \hbox (32.36969pt too wide) in paragraph at lines 3542--3549 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [60] Overfull \hbox (32.36969pt too wide) in paragraph at lines 3617--3624 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [61] Overfull \hbox (3.36687pt too wide) in paragraph at lines 3677--3683 \T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 . Overfull \hbox (14.32507pt too wide) in paragraph at lines 3677--3683 \T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com parators [62] [63] Overfull \hbox (95.20969pt too wide) in paragraph at lines 3848--3860 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [64] [65] Overfull \hbox (32.36969pt too wide) in paragraph at lines 3964--3971 []\T1/ptm/m/n/10 Other Plot-ting func-tions: [][]\T1/zi4/m/n/10 CIS_volcano_plo t[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 HSC_population_plot[][][]()\T1/ptm /m/n/10 , [][]\T1/zi4/m/n/10 circos_genomic_density[][][]()\T1/ptm/m/n/10 , [66] Overfull \hbox (12.649pt too wide) in paragraph at lines 4000--4002 []\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns Overfull \hbox (95.20969pt too wide) in paragraph at lines 4047--4059 []\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][] []()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n /10 cumulative_count_union[][][]()\T1/ptm/m/n/10 , [67] Overfull \hbox (99.30962pt too wide) in paragraph at lines 4114--4118 []\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix [][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T 1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]() [68] (/tmp/RtmpR4QPxb/Rbuild13fdf567ab114b/ISAnalytics/.Rd2pdf1310197/Rd2.ind [69] Overfull \hbox (3.3567pt too wide) in paragraph at lines 43--45 []| \T1/zi4/m/n/10 clinical_relevant_suspicious_genes\T1/ptm/m/n/10 , [70] Overfull \hbox (23.3567pt too wide) in paragraph at lines 219--222 []\T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 , LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined (Font) using `T1/zi4/m/n' instead on input line 302. [71]) (/tmp/RtmpR4QPxb/Rbuild13fdf567ab114b/ISAnalytics/.Rd2pdf1310197/Rd2.aux) LaTeX Font Warning: Some font shapes were not available, defaults substituted. ) (see the transcript file for additional information)pdfTeX warning (dest): name {Rfn.dynamic.Rdash.dots} has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.glue} has been referenced but does not exist, r eplaced by a fixed one pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.auto } has been referenced but does not exist, replaced by a fixed one pdfTeX warning (dest): name{Rfn.import.Rul.parallel.Rul.Vispa2Matrices.Rul.inte ractive} has been referenced but does not exist, replaced by a fixed one {/usr/share/texlive/texmf-dist/fonts/enc/dvips/inconsolata/i4-ts1.enc}{/us r/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc}{/usr/share/texlive/texm f-dist/fonts/enc/dvips/inconsolata/i4-t1-0.enc} Output written on Rd2.pdf (71 pages, 245283 bytes). Transcript written on Rd2.log. Saving output to ‘/tmp/RtmpR4QPxb/Rbuild13fdf567ab114b/ISAnalytics/build/ISAnalytics.pdf’ ... Done * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘ISAnalytics_1.4.3.tar.gz’