footprintsScanner {ATACseqQC} | R Documentation |
Aggregate ATAC-seq footprint for a bunch of motifs generated over binding sites within the genome.
footprintsScanner(bamExp, bamCtl, indexExp = bamExp, indexCtl = bamCtl, bindingSitesList, seqlev = paste0("chr", c(1:25, "X", "Y")), proximal = 45L, distal = proximal, gap = 5L)
bamExp |
A vector of characters indicates the file names of experiment bams. The bam file must be the one with shifted reads. |
bamCtl |
A vector of characters indicates the file names of control bams. The bam file must be the one with shifted reads. |
indexExp, indexCtl |
The names of the index file of the 'BAM' file being processed; This is given without the '.bai' extension. |
bindingSitesList |
A object of GRangesList indicates candidate binding sites (eg. the output of fimo). |
seqlev |
A vector of characters indicates the sequence levels. |
proximal, distal |
numeric(1) or integer(1). basepair for open region from binding sites (proximal) and extented region for background (distal) of the binding region for aggregate ATAC-seq footprint. |
gap |
numeric(1) or integer(1). basepair for gaps among binding sites, proximal, and distal. default is 5L. |
a list. It includes: - bindingSites GRanges of binding site with hits of reads - data a list with test result for each binding site - results a data.frame with open score and enrichment score of motifs
Jianhong Ou
bamfile <- system.file("extdata", "GL1.bam", package="ATACseqQC") bsl <- system.file("extdata", "jolma2013.motifs.bindingList.95.rds", package="ATACseqQC") bindingSitesList <- readRDS(bsl) footprintsScanner(bamfile, seqlev="chr1", bindingSitesList=bindingSitesList)