pseudoPausingIndex: Simulation pausing index

In jianhong/ATACseqQC: ATAC-seq Quality Control

Simulation pausing index

Description

The polII pausing index is the ratio of the reads density at the 5' end of the gene to that in the gene body. This function will simulate the pausing index by open chromatin coverage instead of PolII signaling. The pausing index is a raio between aggregate distribution of reads in TSS and that elongating gene bodys. The default PI = [average coverage of TSS (+1 to +200bp) - average coverage of avoidance region (+21 to +60bp)] / the average coverage of in transcripts (+401bp to 600bp).

Usage

pseudoPausingIndex(
  obj,
  txs,
  seqlev = intersect(seqlevels(obj), seqlevels(txs)),
  nascentRegion = c(-200, -1),
  pausedRegion = c(1, 200),
  avoidanceRegion = c(21, 60),
  elongationRegion = c(401, 600),
  pseudocount = 1L
)

Arguments

obj	an object of GAlignments
txs	GRanges of transcripts
seqlev	A vector of characters indicates the sequence levels.
nascentRegion, pausedRegion, avoidanceRegion, elongationRegion	numeric(2) or integer(2). The start and end position of the pre-initiation complex, paused complex, paused complex avoidance region and productive elongation.
pseudocount	numeric(1) or integer(1). Pseudocount. Default is 1.

Value

A object of GRanges with pseudo pausing index.

Author(s)

Jianhong Ou

References

https://doi.org/10.1098 https://www.nature.com/articles/nmeth.2688/figures/3

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)
ppi <- pseudoPausingIndex(gal1, txs)

jianhong/ATACseqQC documentation built on March 19, 2024, 8:30 a.m.