getWeightedBindingScore: Calculate the weighted binding score

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

Calculate the weighted binding score

Description

Use user predefined weight to get the weighted binding score or use open score to weight the binding score. The open score is calculated by the counts of proximal region divided by the counts of distal region. The binding score is calculated by the counts of proximal region divided by the counts of binding region. This value is the measure of avoidance of reads in the binding sites.

Usage

getWeightedBindingScore(se, weight = NA, ...)

Arguments

se	An RangedSummarizedExperiment object. Outputs of countsNormalization.
weight	If NA, the weight will be calculated by the open score. See calWeights. User can define the weight by a matrix or numeric vector.
...	The parameters will be passed to calWeights.

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
se <- countsNormalization(se, proximal=40, distal=40)
## get the weighted binding scores
getWeightedBindingScore(se)

jianhong/ATACseqTFEA documentation built on Feb. 9, 2024, 4:09 a.m.