This package aims to quantify and remove putative double strand DNA from a strand-specific RNA sample. There are also options and methods to plot the positive/negative proportions of all sliding windows, which allow users to have an idea of how much the sample was contaminated and the appropriate threshold to be used for filtering.
The package has some following main functions:
getStrandFromBamFile: calculate positive/negative proprortion and
sum of reads over all sliding windows from a bam file
plotHist: plot histogram of positive proportion of windows
plotWin: plot positive proportion vs number of reads of
windows calculated from
filterDNA: filter a bam file
Thu-Hien To & Steve Pederson
Maintainer: Thu-Hien To <email@example.com>
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