getWinOverlapEachReadFragment: Get the window ranges that overlap each read fragment

In UofABioinformaticsHub/strandCheckR: Calculate strandness information of a bam file

Description

Calculate the window ranges that overlap each read fragment

Usage

getWinOverlapEachReadFragment(readInfo, strand, winWidth, winStep,
  readProp, useCoverage = FALSE, subset = NULL)

Arguments

readInfo	a list contains the read information
strand	the considering strand
winWidth	the width of the sliding window, 1000 by default.
winStep	the step length to sliding the window, 100 by default.
readProp	a read fragment is considered to be included in a window if and only if at least readProp percent of it is in the window.
useCoverage	either base on coverage or number of reads
subset	if we consider only a subset of the input reads

Value

If useCoverage=FALSE: an IRanges object which contains the range of sliding windows that overlap each read fragment. If useCoverage=TRUE: a list of two objects, the first one is the later IRanges object, the second one is an integer-Rle object which contains the coverage of the input readInfo

Examples

library(Rsamtools)
file <- system.file('extdata','s2.sorted.bam',package = 'strandCheckR')
readInfo <- scanBam(file, param = 
ScanBamParam(what = c("pos","cigar","strand")))
getWinOverlapEachReadFragment(readInfo[[1]],"+",1000,100,0.5)

UofABioinformaticsHub/strandCheckR documentation built on Aug. 15, 2021, 9:08 a.m.