footprintsScanner {ATACseqQC} | R Documentation

## scan ATAC-seq footprints infer factor occupancy genome wide

### Description

Aggregate ATAC-seq footprint for a bunch of motifs generated over binding sites within the genome.

### Usage

    footprintsScanner(
      bamExp,
      bamCtl,
      indexExp = bamExp,
      indexCtl = bamCtl,
      bindingSitesList,
      seqlev = paste0("chr", c(1:25, "X", "Y")),
      proximal = 40L,
      distal = proximal,
      gap = 10L,
      maximalBindingWidth = NA,
      cutoffLogFC = log2(1.5),
      cutoffPValue = 0.05,
      correlatedFactorCutoff = 3/4
    )

    prepareBindingSitesList(
      pfms,
      genome,
      seqlev = paste0("chr", c(1:22, "X", "Y")),
      expSiteNum = 5000
    )

### Arguments

`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.
`maximalBindingWidth` | numeric(1) or integer(1). Maximal binding sites width for all the motifs. If setted, all motif binding sites will be re-sized to this value.
`cutoffLogFC, cutoffPValue` | numeric(1). Cutoff value for differential bindings.
`correlatedFactorCutoff` | numeric(1). Cutoff value for correlated factors. If the overlapping binding site within 100bp is more than cutoff, the TFs will be treated as correlated factors.
`pfms` | A list of Position frequency Matrix represented as a numeric matrix with row names A, C, G and T.
`genome` | An object of BSgenome.
`expSiteNum` | numeric(1). Expect number of predicted binding sites. if predicted binding sites is more than this number, top expSiteNum binding sites will be used.

### Value

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

### Author(s)

Jianhong Ou

### Examples

    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)

    library(MotifDb)
    motifs <- query(MotifDb, c("Hsapiens"))
    motifs <- as.list(motifs)
    library(BSgenome.Hsapiens.UCSC.hg19)
    #bindingSitesList <- prepareBindingSitesList(motifs, genome=Hsapiens)

[Package ATACseqQC version 1.11.8 Index]