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

Description Usage Arguments Value See Also Examples

View source: R/getStrandFromReadInfo.R

Description

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

Usage

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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

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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/rnaCleanR documentation built on July 12, 2019, 10 p.m.