ATACseqQC: ATAC-seq Quality Control

PTscore

R Documentation

Promoter/Transcript body (PT) score

Description

PT score is calculated for coverage of promoter divided by the coverage of transcripts body. PT score will show if the signal is enriched in promoters.

Usage

PTscore(
  obj,
  txs,
  seqlev = intersect(seqlevels(obj), seqlevels(txs)),
  upstream = 2000,
  downstream = 500
)

Arguments

`obj`	an object of GAlignments
`txs`	GRanges of transcripts
`seqlev`	A vector of characters indicates the sequence levels.
`upstream`	numeric(1) or integer(1). Start position of promoter. Default is 2000
`downstream`	numeric(1) or integer(1). End position of promoter. Default is 500

Value

A object of GRanges with PT scores

Author(s)

Jianhong Ou

Examples

 
library(GenomicRanges)
bamfile <- system.file("extdata", "GL1.bam", 
                       package="ATACseqQC", mustWork=TRUE)
gal1 <- readBamFile(bamFile=bamfile, tag=character(0), 
                    which=GRanges("chr1", IRanges(1, 1e6)), 
                    asMates=FALSE)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txs <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene)
pt <- PTscore(gal1, txs)

jianhong/ATACseqQC documentation built on Nov. 2, 2024, 12:08 a.m.