strandCheckR-package: Quantify and Filter putative double strand DNA from...
In strandCheckR: Calculate strandness information of a bam file

Description Details Author(s) Examples

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:

- getWinFromBamFile: calculate positive/negative proprortion and sum of reads over all sliding windows from a bam file

- plotHist: plot histogram of positive proportion of windows calculated from getWinFromBamFile method

- plotWin: plot positive proportion vs number of reads of windows calculated from getWinFromBamFile method

- filterDNA: filter a bam file

Thu-Hien To & Steve Pederson

Maintainer: Hien To <hien.to@adelaide.edu.au>

bamfilein <- system.file("extdata","s1.sorted.bam",package = "strandCheckR")
windows <- getWinFromBamFile(bamfilein)
plotWin(windows)
plotHist(windows)
filterDNA(file = bamfilein,destination = "filter.bam")