getWinOfAlignments {strandCheckR}R Documentation

get the window ranges of alignments

Description

calculate the windows that contain each read fragment

Usage

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

Arguments

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

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


[Package strandCheckR version 1.8.0 Index]