Transcription Start Site (TSS) Enrichment Score

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,
  width = 100,
  step = width,
  pseudocount = 0
)

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
width	numeric(1) or integer(1). the window size for TSS score. Default is 100.
step	numeric(1) or integer(1). The distance between the start position of the sliding windows.
pseudocount	numeric(1) or integer(1). Pseudocount. Default is 0. If pseudocount is no greater than 0, the features with ZERO or less than ZERO counts in flank region will be removed in calculation.

Value

A object of GRanges with TSS scores

References

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

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)
tsse <- TSSEscore(gal1, txs)