countsNormalization: Normalize counts by width of count region

In jianhong/ATACseqTFEA: Transcription Factor Enrichment Analysis for ATAC-seq

Normalize counts by width of count region

Description

Do normalization by width for counts in binding sites, proximal and distal regions.

Usage

countsNormalization(se, proximal, distal)

Arguments

se	An RangedSummarizedExperiment object. Outputs of count5ends or eventsFilter.
proximal, distal	numeric(1) or integer(1). bases for open region from binding sites (proximal) and extended region for background (distal) of the binding region for aggregate ATAC-seq footprint.

Value

A RangedSummarizedExperiment object with assays of count matrix with bindingSites, proximalRegion and distalRegion as column names and bindingSites GRanges object as rowRanges.

Author(s)

Jianhong Ou

Examples

bam <- system.file("extdata",
                   "KD.shift.rep1.bam",
                   package="ATACseqTFEA")
bsl <- system.file("extdata", "bindingSites.rds",
                   package="ATACseqTFEA")
bindingSites <- readRDS(bsl)
## get the count regions
bsEx <- expandBindingSites(bindingSites)
## count reads by 5'ends
res <- count5ends(bam, positive=0L, negative=0L,
                  bindingSites=bindingSites,
                  bindingSitesWithGap=bsEx$bindingSitesWithGap,
                  bindingSitesWithProximal=bsEx$bindingSitesWithProximal,
                  bindingSitesWithProximalAndGap=
                      bsEx$bindingSitesWithProximalAndGap,
                  bindingSitesWithDistal=bsEx$bindingSitesWithDistal)
## filter 0 counts in proximal
se <- eventsFilter(res, proximalRegion>0)
## normalize counts by width of count region
countsNormalization(se, proximal=40, distal=40)

jianhong/ATACseqTFEA documentation built on Nov. 5, 2024, 9:46 a.m.