TSSEscore {ATACseqQC} | R Documentation |
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 (each step within 1000 bp each side) / the depth of end flanks (100bp each end). TSSE score = max(mean(TSS score in each window)).
TSSEscore( obj, txs, seqlev = intersect(seqlevels(obj), seqlevels(txs)), upstream = 1000, downstream = 1000, endSize = 100 )
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 |
A object of GRanges with TSS scores
Jianhong Ou
https://www.encodeproject.org/data-standards/terms/#enrichment
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)