Promoter/Transcript body (PT) score — PTscore • ATACseqQC

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.

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

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)