Package index • strandCheckR

Check Stranded Alignments

getStrandFromBamFile(): Get the strand information of all windows from bam files

getStrandFromReadInfo(): Get the strand information of all windows from read information

getWinOverlapEachIRange(): Get the ranges of sliding windows that overlap each range of an IRanges object.

getWinOverlapEachReadFragment(): Get the window ranges that overlap each read fragment

getWinOverlapGRanges(): Get the sliding windows that overlap a GRanges object

plotHist(): Plot the histogram of positive proportions

plotWin(): Plot the number of reads vs the proportion of '+' stranded reads.

checkPairedEnd(): Test whether a bam file is single-end or paired-end

filterDNA(): Filter reads comming from double strand sequences from a bam File

intersectWithFeature(): Intersect the windows data frame with an annotation data frame

strandCheckR-package strandCheckR: Quantify and Filter putative double strand DNA from strand-specific RNA bam file