getStrandFromReadInfo {strandCheckR} | R Documentation |
Get the number of positive/negative reads of all windows from
read information obtained from scanBam
function
getStrandFromReadInfo(readInfo, winWidth = 1000L, winStep = 100L, readProp = 0.5, subset = NULL)
readInfo |
a list contains read information returned by
|
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
|
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)