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.
