getWinFromReadInfo: get the strand information of all windows from read...

In 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

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

Arguments

readInfo	a list contains read information returned by scanBam function when read a bam file
winWidth	the width 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, getWinFromBamFile

strandCheckR documentation built on Nov. 8, 2020, 7:02 p.m.