getStrandFromReadInfo: Get the strand information of all windows from read...

In UofABioinformaticsHub/strandCheckR: Calculate strandness information of a bam file

Description

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

Usage

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

Arguments

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

Value

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

See Also

filterDNA, getStrandFromBamFile

Examples

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)

UofABioinformaticsHub/strandCheckR documentation built on Aug. 15, 2021, 9:08 a.m.