getWinOfAlignments {strandCheckR} | R Documentation |
calculate the windows that contain each read fragment
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 |
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