getStrandFromReadInfo: Get the strand information of all windows from read...
In UofABioinformaticsHub/rnaCleanR: Calculate strandness information of a bam file

Description Usage Arguments Value See Also Examples

Get the number of positive/negative reads of all windows from read information obtained from scanBam function

1 2	getStrandFromReadInfo(readInfo, winWidth = 1000L, winStep = 100L, readProp = 0.5, subset = NULL)

`readInfo`	a list contains read information returned by `scanBam` function when read a bam file.
`winWidth`	the length of the sliding window, 1000 by default.
`winStep`	the step length to sliding the window, 100 by default.
`readProp`	A read is considered to be included in a window if at least `readProp` of it is in the window. Specified as a proportion. 0.5 by default.
`subset`	an integer vector specifying the subset of reads to consider

a DataFrame object containing the number of positive/negative reads and coverage of each window sliding .

filterDNA, getStrandFromBamFile

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