strandCheckR-package: Quantify and Filter putative double strand DNA from...
In UofABioinformaticsHub/strandCheckR: Calculate strandness information of a bam file
Description
Details
Author(s)
Examples
Description
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.
Details
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
calculated from getStrandFromBamFile method
- plotWin: plot positive proportion vs number of reads of
windows calculated from getStrandFromBamFile method
- filterDNA: filter a bam file
Author(s)
Thu-Hien To & Steve Pederson
Maintainer: Thu-Hien To <tothuhien@gmail.com>
Examples
1
2
3
4
5
bamfilein <- system.file("extdata","s1.sorted.bam",package = "strandCheckR")
windows <- getStrandFromBamFile(bamfilein)
plotWin(windows)
plotHist(windows)
filterDNA(file = bamfilein,destination = "filter.bam")
UofABioinformaticsHub/strandCheckR documentation built on Aug. 15, 2021, 9:08 a.m.
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Description Details Author(s) Examples
Description
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.
Details
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
calculated from getStrandFromBamFile method
- plotWin: plot positive proportion vs number of reads of
windows calculated from getStrandFromBamFile method
- filterDNA: filter a bam file
Author(s)
Thu-Hien To & Steve Pederson
Maintainer: Thu-Hien To <tothuhien@gmail.com>
Examples
1 2 3 4 5 | bamfilein <- system.file("extdata","s1.sorted.bam",package = "strandCheckR")
windows <- getStrandFromBamFile(bamfilein)
plotWin(windows)
plotHist(windows)
filterDNA(file = bamfilein,destination = "filter.bam")
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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