doTFEA: Transcription factor enrichment analysis

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

Transcription factor enrichment analysis

Description

Transcription factor enrichment analysis for the filtered output of DBscore

Usage

doTFEA(se, ...)

Arguments

se	An RangedSummarizedExperiment object. Filtered outputs of DBscore.
...	Not used.

Value

A TFEAresults object.

Author(s)

Jianhong Ou

Examples

bamExp <- system.file("extdata",
                      c("KD.shift.rep1.bam",
                        "KD.shift.rep2.bam"),
                      package="ATACseqTFEA")
bamCtl <- system.file("extdata",
                      c("WT.shift.rep1.bam",
                        "WT.shift.rep2.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(c(bamExp, bamCtl),
                  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
se <- getWeightedBindingScore(se)
design <- cbind(CTL=1, EXPvsCTL=c(1, 1, 0, 0))
rownames(design) <- colnames(se)
counts <- DBscore(se, design=design, coef="EXPvsCTL")
doTFEA(counts)

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