Contents

1 Introduction

Sequence-based TF affinity scoring can be conducted with the FIMO suite, see @Sonawane2017. We have serialized an object with references to FIMO outputs for 16 TFs.

## GenomicFiles object with 1 ranges and 16 files: 
## files: M0635_1.02sort.bed.gz, M3433_1.02sort.bed.gz, ..., M6159_1.02sort.bed.gz, M6497_1.02sort.bed.gz 
## detail: use files(), rowRanges(), colData(), ...

While the token bed is used in the filenames, the files are not actually bed format!

2 Importing with scanTabix

We can use reduceByRange to import selected scans.

## List of 1
##  $ :List of 2
##   ..$ POU2F1:List of 1
##   .. ..$ chr17:38077000-38084000: chr [1:12] "chr17\t38077313\t38077331\tchr17:38077313-38077331\t2.15306\t+\t0.000352" "chr17\t38078549\t38078567\tchr17:38078549-38078567\t0.102041\t-\t0.000634" "chr17\t38078556\t38078574\tchr17:38078556-38078574\t-0.0408163\t-\t0.00066" "chr17\t38080045\t38080063\tchr17:38080045-38080063\t1.66327\t-\t0.000407" ...
##   ..$ VDR   :List of 1
##   .. ..$ chr17:38077000-38084000: chr [1:18] "chr17\t38077445\t38077460\tchr17:38077445-38077460\t-1.9899\t-\t0.000666" "chr17\t38078536\t38078551\tchr17:38078536-38078551\t-2.66667\t-\t0.0008" "chr17\t38078574\t38078589\tchr17:38078574-38078589\t1.65657\t+\t0.000235" "chr17\t38078796\t38078811\tchr17:38078796-38078811\t2.07071\t-\t0.000207" ...

This result can be massaged into a GRanges or other desirable structure. fimo_granges takes care of this.

## $POU2F1
## $POU2F1$`chr17:38070000-38090000`
## GRanges object with 76 ranges and 4 metadata columns:
##        seqnames            ranges strand |                  rname      score
##           <Rle>         <IRanges>  <Rle> |            <character>  <numeric>
##    [1]    chr17 38070239-38070257      * | chr17:38070239-38070.. -1.5408200
##    [2]    chr17 38070579-38070597      * | chr17:38070579-38070.. -0.9693880
##    [3]    chr17 38070851-38070869      * | chr17:38070851-38070..  0.1224490
##    [4]    chr17 38071025-38071043      * | chr17:38071025-38071..  0.0918367
##    [5]    chr17 38071253-38071271      * | chr17:38071253-38071..  3.6734700
##    ...      ...               ...    ... .                    ...        ...
##   [72]    chr17 38088602-38088620      * | chr17:38088602-38088..    4.06122
##   [73]    chr17 38088637-38088655      * | chr17:38088637-38088..   11.69390
##   [74]    chr17 38089141-38089159      * | chr17:38089141-38089..   13.18370
##   [75]    chr17 38089439-38089457      * | chr17:38089439-38089..   -1.35714
##   [76]    chr17 38089822-38089840      * | chr17:38089822-38089..    3.67347
##                dir      pval
##        <character> <numeric>
##    [1]           +  0.000989
##    [2]           -  0.000849
##    [3]           -  0.000631
##    [4]           -  0.000636
##    [5]           +  0.000222
##    ...         ...       ...
##   [72]           +  1.98e-04
##   [73]           -  1.32e-05
##   [74]           -  7.09e-06
##   [75]           -  9.42e-04
##   [76]           -  2.22e-04
##   -------
##   seqinfo: 1 sequence from hg19 genome
## 
## 
## $VDR
## $VDR$`chr17:38070000-38090000`
## GRanges object with 40 ranges and 4 metadata columns:
##        seqnames            ranges strand |                  rname      score
##           <Rle>         <IRanges>  <Rle> |            <character>  <numeric>
##    [1]    chr17 38070016-38070031      * | chr17:38070016-38070..  0.0505051
##    [2]    chr17 38070387-38070402      * | chr17:38070387-38070.. -3.3838400
##    [3]    chr17 38070925-38070940      * | chr17:38070925-38070..  5.7171700
##    [4]    chr17 38071183-38071198      * | chr17:38071183-38071.. -0.6767680
##    [5]    chr17 38072289-38072304      * | chr17:38072289-38072.. -0.3333330
##    ...      ...               ...    ... .                    ...        ...
##   [36]    chr17 38086915-38086930      * | chr17:38086915-38086..  -0.353535
##   [37]    chr17 38087304-38087319      * | chr17:38087304-38087..   0.101010
##   [38]    chr17 38087866-38087881      * | chr17:38087866-38087..   5.343430
##   [39]    chr17 38088893-38088908      * | chr17:38088893-38088..  -0.111111
##   [40]    chr17 38089214-38089229      * | chr17:38089214-38089..   1.101010
##                dir      pval
##        <character> <numeric>
##    [1]           +  3.77e-04
##    [2]           +  9.66e-04
##    [3]           -  6.44e-05
##    [4]           +  4.63e-04
##    [5]           -  4.21e-04
##    ...         ...       ...
##   [36]           -  0.000423
##   [37]           -  0.000371
##   [38]           +  0.000073
##   [39]           -  0.000395
##   [40]           -  0.000277
##   -------
##   seqinfo: 1 sequence from hg19 genome
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] grid      stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] UpSetR_1.4.0                magrittr_2.0.1             
##  [3] dplyr_1.0.7                 gwascat_2.25.0             
##  [5] GSEABase_1.55.2             graph_1.71.2               
##  [7] annotate_1.71.0             XML_3.99-0.8               
##  [9] png_0.1-7                   ggplot2_3.3.5              
## [11] knitr_1.36                  data.table_1.14.2          
## [13] GO.db_3.14.0                GenomicFiles_1.29.0        
## [15] rtracklayer_1.53.1          Rsamtools_2.9.1            
## [17] Biostrings_2.61.2           XVector_0.33.0             
## [19] BiocParallel_1.27.17        SummarizedExperiment_1.23.5
## [21] GenomicRanges_1.45.0        GenomeInfoDb_1.29.10       
## [23] MatrixGenerics_1.5.4        matrixStats_0.61.0         
## [25] org.Hs.eg.db_3.14.0         AnnotationDbi_1.55.2       
## [27] IRanges_2.27.2              S4Vectors_0.31.5           
## [29] Biobase_2.53.0              BiocGenerics_0.39.2        
## [31] TFutils_1.13.4              BiocStyle_2.21.4           
## 
## loaded via a namespace (and not attached):
##  [1] colorspace_2.0-2         rjson_0.2.20             ellipsis_0.3.2          
##  [4] farver_2.1.0             bit64_4.0.5              fansi_0.5.0             
##  [7] xml2_1.3.2               codetools_0.2-18         splines_4.1.1           
## [10] snpStats_1.43.1          cachem_1.0.6             jsonlite_1.7.2          
## [13] dbplyr_2.1.1             shiny_1.7.1              BiocManager_1.30.16     
## [16] readr_2.0.2              compiler_4.1.1           httr_1.4.2              
## [19] assertthat_0.2.1         Matrix_1.3-4             fastmap_1.1.0           
## [22] later_1.3.0              htmltools_0.5.2          prettyunits_1.1.1       
## [25] tools_4.1.1              gtable_0.3.0             glue_1.4.2              
## [28] GenomeInfoDbData_1.2.7   rappdirs_0.3.3           Rcpp_1.0.7              
## [31] cellranger_1.1.0         jquerylib_0.1.4          vctrs_0.3.8             
## [34] xfun_0.27                stringr_1.4.0            mime_0.12               
## [37] miniUI_0.1.1.1           lifecycle_1.0.1          restfulr_0.0.13         
## [40] zlibbioc_1.39.0          scales_1.1.1             BSgenome_1.61.0         
## [43] VariantAnnotation_1.39.0 hms_1.1.1                promises_1.2.0.1        
## [46] parallel_4.1.1           yaml_2.2.1               curl_4.3.2              
## [49] gridExtra_2.3            memoise_2.0.0            sass_0.4.0              
## [52] biomaRt_2.49.7           stringi_1.7.5            RSQLite_2.2.8           
## [55] highr_0.9                BiocIO_1.3.0             GenomicFeatures_1.45.2  
## [58] filelock_1.0.2           rlang_0.4.12             pkgconfig_2.0.3         
## [61] bitops_1.0-7             evaluate_0.14            lattice_0.20-45         
## [64] purrr_0.3.4              labeling_0.4.2           GenomicAlignments_1.29.0
## [67] bit_4.0.4                tidyselect_1.1.1         bookdown_0.24           
## [70] plyr_1.8.6               R6_2.5.1                 generics_0.1.0          
## [73] DelayedArray_0.19.4      DBI_1.1.1                pillar_1.6.4            
## [76] withr_2.4.2              survival_3.2-13          KEGGREST_1.33.0         
## [79] RCurl_1.98-1.5           tibble_3.1.5             crayon_1.4.1            
## [82] utf8_1.2.2               BiocFileCache_2.1.1      tzdb_0.1.2              
## [85] rmarkdown_2.11           progress_1.2.2           readxl_1.3.1            
## [88] blob_1.2.2               digest_0.6.28            xtable_1.8-4            
## [91] httpuv_1.6.3             munsell_0.5.0            bslib_0.3.1