getWinOfAlignments: get the window ranges of alignments
In strandCheckR: Calculate strandness information of a bam file

calculate the windows that contain each read fragment

1 2	getWinOfAlignments(readInfo, strand, winWidth, winStep, readProp, useCoverage = FALSE, subset = NULL)

`readInfo`	a list contains the read information of one sequence
`strand`	the considering strand
`winWidth`	the window size
`winStep`	the window winStep
`readProp`	a read 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

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

strandCheckR documentation built on Nov. 8, 2020, 7:02 p.m.