PTscore {ATACseqQC} | 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)

[Package ATACseqQC version 1.10.4 Index]