Calculate strandness information of a bam file


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Documentation for package ‘strandCheckR’ version 1.0.0

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strandCheckR-package Quantify and Filter putative double strand DNA from strand-specific RNA bam file
calculateStrandCoverage Calculate the strand information based on coverage
calculateStrandNbReads Calculate the strand information based the number of reads
checkPairedEnd Test whether a bam file if single end or paired end
concatenateAlignments Concatenate a list of Alignments into One
filterDNA Filter Double Strand Sequences from a Bam File
getWinFromBamFile get the strand information of all windows from bam files
getWinFromGranges Get the Sliding Windows from a GRanges object
getWinFromIRanges Get the Ranges of Sliding Windows from an IRanges object
getWinFromReadInfo get the strand information of all windows from read information
getWinOfAlignments get the window ranges of alignments
intersectWithFeature Intersect the windows data frame with an annotation data frame
keptProbaWin get the probability of begin kept for each window
keptReadFragment calculate the read fragments to be kept
plotHist Plot the histogram of positive proportions
plotWin Plot the Proportion of + Stranded Reads
strandCheckR Quantify and Filter putative double strand DNA from strand-specific RNA bam file
summarizeHist Summarize the histogram of strand proportions from the input windows data frame