Calculate strandness information of a bam file

---

Documentation for package ‘strandCheckR’ version 1.27.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

strandCheckR-package	Quantify and Filter putative double strand DNA from strand-specific RNA bam file
checkPairedEnd	Test whether a bam file is single-end or paired-end
filterDNA	Filter reads comming from double strand sequences from a bam File
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
intersectWithFeature	Intersect the windows data frame with an annotation data frame
plotHist	Plot the histogram of positive proportions
plotWin	Plot the number of reads vs the proportion of '+' stranded reads.
strandCheckR	Quantify and Filter putative double strand DNA from strand-specific RNA bam file