TSSEscore {ATACseqQC} | R Documentation

## Transcription Start Site (TSS) Enrichment Score

### Description

TSS score is a raio between aggregate distribution of reads centered on TSSs and that flanking the corresponding TSSs. TSS score = the depth of TSS (1000 bp each side) / the depth of end flanks (100bp each end).

### Usage

    TSSEscore(
      obj,
      txs,
      seqlev = intersect(seqlevels(obj), seqlevels(txs)),
      upstream = 1000,
      downstream = 1000,
      endSize = 100
    )

### Arguments

`obj` | an object of GAlignments
`txs` | GRanges of transcripts
`seqlev` | A vector of characters indicates the sequence levels.
`upstream, downstream` | numeric(1) or integer(1). upstream and downstream of TSS. Default is 1000
`endSize` | numeric(1) or integer(1). the size of the end flanks. Default is 100

### Value

A object of GRanges with TSS scores

### Author(s)

Jianhong Ou

### References

https://www.encodeproject.org/data-standards/terms/#enrichment

### 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)
    tsse <- TSSEscore(gal1, txs)

[Package ATACseqQC version 1.10.4 Index]