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This page was generated on 2021-11-24 15:05:04 -0500 (Wed, 24 Nov 2021).

BUILD results for ISAnalytics on nebbiolo2

To the developers/maintainers of the ISAnalytics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ISAnalytics.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 956/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISAnalytics 1.4.1  (landing page)
Andrea Calabria
Snapshot Date: 2021-11-23 04:15:06 -0500 (Tue, 23 Nov 2021)
git_url: https://git.bioconductor.org/packages/ISAnalytics
git_branch: RELEASE_3_14
git_last_commit: 0fed8b9
git_last_commit_date: 2021-10-28 05:05:55 -0500 (Thu, 28 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ISAnalytics
Version: 1.4.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ISAnalytics
StartedAt: 2021-11-23 06:40:10 -0500 (Tue, 23 Nov 2021)
EndedAt: 2021-11-23 06:40:42 -0500 (Tue, 23 Nov 2021)
EllapsedTime: 31.6 seconds
RetCode: 0
Status:   OK  
PackageFile: ISAnalytics_1.4.1.tar.gz
PackageFileSize: 4.218 MiB

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ISAnalytics
###
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* 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)
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\T1/ptm/m/n/10 group. For more de-tails on how to use this func-tion: \T1/zi4/m
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\T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun
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[]\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 ,
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[]\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 ,

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\T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 circlize::circos.genomicLabels() 

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[]\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 ,
[10]
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] 
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[]\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)
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[]\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 ,
[14]
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[]\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[][][]
[15] [16]
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[]\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()

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\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]
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\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]
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[]\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 ,

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[][]\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 ,
[20] [21]
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[]\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 ,

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[][]\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 ,

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[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-

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\T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it
/10 ,

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\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
[22] [23] [24] [25]
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[]\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[][][]() 
[26]
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[]\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",

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[]\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[][][]() 
[27]
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[]\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
 ,
[28]
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[]\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match
-ing is case-insensitive. 
[29] [30]
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\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 . 
[31]
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[]\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[][][]() 
[32]
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\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 . 

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[]\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

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[]\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[][][]() 
[33]
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[]\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

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[]\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[][][]() 
[34]
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\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[][][]. 

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\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 . 
[35] [36]
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[]\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 ,
[37] [38]
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[]\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 ,

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[][]\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 ,
[39] [40]
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[]\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

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[]\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 ,

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[][]\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 ,
[41] [42]
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[]\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 . 
[43]
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\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 . 
[44] [45] [46] [47] [48]
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[]\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 ,

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[][]\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 ,

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[]\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
[49]
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\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 ,

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[]\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() 

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[]\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
[50] [51] (/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd)
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\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

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[]\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() 
[53]
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\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 . 
[54]
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[]\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 ,

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[][]\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 ,
[55] [56]
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[]\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 ,
[57]
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[]\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 ,
[58]
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[]\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]
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\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 .

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\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
[60] [61]
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[]\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 ,
[62] [63]
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[]\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 ,
[64]
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[]\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

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[]\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 ,
[65]
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[]\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[][][]() 
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\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
[4]
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\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
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[]\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]
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[]\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 ,

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\T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 circlize::circos.genomicLabels() 

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[]\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 ,
[11]
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] 
[12]
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[]\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)
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[]\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]
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[]\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] [17]
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[]\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()

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\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]
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\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]
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[]\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 ,

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[][]\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] [22]
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[]\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 ,

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[][]\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 ,

Underfull \hbox (badness 10000) in paragraph at lines 1346--1346
[]\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 1346--1346
\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 1346--1346
\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 1531--1535
[]\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 1582--1587
[]\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 1597--1601
[]\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 1649--1656
[]\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]
Overfull \hbox (3.4271pt too wide) in paragraph at lines 1739--1741
[]\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match
-ing is case-insensitive. 
[30] [31]
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\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 . 
[32]
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[]\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]
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\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 1948--1950
[]\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

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[]\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 2021--2023
[]\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

Overfull \hbox (100.40988pt too wide) in paragraph at lines 2030--2034
[]\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[][][]() 
[35]
Overfull \hbox (3.81735pt too wide) in paragraph at lines 2079--2082
\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[][][]. 

Overfull \hbox (5.10971pt too wide) in paragraph at lines 2091--2094
\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 . 
[36] [37]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 2210--2217
[]\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 ,
[38] [39]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2332--2344
[]\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 2332--2344
[][]\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 2432--2437
[]\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

Overfull \hbox (95.20969pt too wide) in paragraph at lines 2460--2472
[]\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 2460--2472
[][]\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 ,
[42] [43]
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[]\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]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 2647--2650
\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 . 
[45] [46] [47] [48] [49]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2904--2916
[]\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 ,

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[][]\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 2939--2943
[]\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]
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\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 ,

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[]\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 3014--3016
[]\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]
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\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

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[]\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() 
[54]
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\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]
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[]\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 ,

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[][]\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]
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[]\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]
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[]\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]
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[]\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]
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\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 .

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\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]
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[]\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]
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[]\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]
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[]\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

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[]\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]
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[]\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]
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\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
[4]
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\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] [7] [8]
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[]\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]
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[]\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 ,

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\T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 circlize::circos.genomicLabels() 

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[]\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 ,
[11]
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] 
[12]
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[]\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)
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[]\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]
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[]\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] [17]
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[]\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()

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\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]
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\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]
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[]\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 ,

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[][]\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] [22]
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[]\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 ,

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[][]\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 ,

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[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-

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\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 1346--1346
\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
[23] [24] [25] [26]
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[]\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]
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[]\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",

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[]\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]
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[]\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]
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[]\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match
-ing is case-insensitive. 
[30] [31]
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\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 . 
[32]
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[]\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]
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\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 . 

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[]\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

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[]\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]
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[]\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

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[]\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[][][]() 
[35]
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\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[][][]. 

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\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 . 
[36] [37]
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[]\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 ,
[38] [39]
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[]\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 ,

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[][]\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]
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[]\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

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[]\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 ,

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[][]\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 ,
[42] [43]
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[]\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]
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\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 . 
[45] [46] [47] [48] [49]
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[]\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 ,

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[][]\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 ,

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[]\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]
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\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 ,

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[]\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() 

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[]\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]
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\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

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[]\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() 
[54]
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\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]
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[]\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 ,

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[][]\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 ,
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[]()\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]
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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]
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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]
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\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 .

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\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
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[]()\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
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[]\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]
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[]()\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
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[]\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[][][]() 
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\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
[4]
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\T1/ptm/m/n/10 the spec-i-fied lambda. For more de-tails on how to use this fun
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[]\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]
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[]\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 ,

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\T1/zi4/m/n/10 circlize::circos.genomicDensity() \T1/ptm/m/n/10 and \T1/zi4/m/n
/10 circlize::circos.genomicLabels() 

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[]\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 ,
[11]
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][] 
[12]
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[]\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)
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[]\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]
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[]\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] [17]
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[]\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()

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\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]
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\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]
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[]\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 ,

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[][]\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] [22]
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[]\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 ,

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[][]\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 ,

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[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-

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/10 ,

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[23] [24] [25] [26]
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[]\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]
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[]\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",

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[]\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[][]
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[28]
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[]\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]
Overfull \hbox (3.4271pt too wide) in paragraph at lines 1739--1741
[]\T1/ptm/m/n/10 The cell types to in-clude in the mod-els. Note that the match
-ing is case-insensitive. 
[30] [31]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 1845--1848
\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 . 
[32]
Overfull \hbox (115.40988pt too wide) in paragraph at lines 1869--1873
[]\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 1932--1935
\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 1948--1950
[]\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 1959--1963
[]\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 2021--2023
[]\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

Overfull \hbox (100.40988pt too wide) in paragraph at lines 2030--2034
[]\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[][][]() 
[35]
Overfull \hbox (3.81735pt too wide) in paragraph at lines 2079--2082
\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[][][]. 

Overfull \hbox (5.10971pt too wide) in paragraph at lines 2091--2094
\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 . 
[36] [37]
Overfull \hbox (32.36969pt too wide) in paragraph at lines 2210--2217
[]\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 ,
[38] [39]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2332--2344
[]\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 2332--2344
[][]\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 2432--2437
[]\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

Overfull \hbox (95.20969pt too wide) in paragraph at lines 2460--2472
[]\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 2460--2472
[][]\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 ,
[42] [43]
Overfull \hbox (51.20859pt too wide) in paragraph at lines 2543--2545
[]\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]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 2647--2650
\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 . 
[45] [46] [47] [48] [49]
Overfull \hbox (95.20969pt too wide) in paragraph at lines 2904--2916
[]\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 2904--2916
[][]\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 2939--2943
[]\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 2987--2994
\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 3004--3006
[]\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 3014--3016
[]\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 3156--3166
\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

Overfull \hbox (33.6188pt too wide) in paragraph at lines 3189--3191
[]\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() 
[54]
Overfull \hbox (5.10971pt too wide) in paragraph at lines 3200--3203
\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]
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[]\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 3299--3311
[][]\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 3381--3393
[]\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 3465--3472
[]\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 3540--3547
[]\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]
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\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 .

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\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]
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[]\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 3887--3894
[]\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 3923--3925
[]\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

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[]\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]
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[]\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] (/tmp/RtmplZE4VB/Rbuild1d15b5fa5ab37/ISAnalytics/.Rd2pdf1906101/Rd2.ind
[68]
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[]| \T1/zi4/m/n/10 clinical_relevant_suspicious_genes\T1/ptm/m/n/10 , 
[69]
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[]\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 299.

[70]) (/tmp/RtmplZE4VB/Rbuild1d15b5fa5ab37/ISAnalytics/.Rd2pdf1906101/Rd2.aux)

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 )
(see the transcript file for additional information)pdfTeX warning (dest): name
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Output written on Rd2.pdf (70 pages, 242379 bytes).
Transcript written on Rd2.log.
Saving output to ‘/tmp/RtmplZE4VB/Rbuild1d15b5fa5ab37/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_1.4.1.tar.gz’