PTscore {ATACseqQC} | R Documentation |
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)
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 |
A object of GRanges with PT scores
Jianhong Ou
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)