In philliplab/hypermutR: Detects hypermutation in DNA

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Overview

hypermutR was originally developed as a replacement for the removeHypermutatedSequences.R script in the hiv-founder-id pipeline which is hosted at Founder Pipeline.

This script is (hopefully was by the time you read this) called from the identify-founders.pl script using perl's backtick notation. Information was passed to the removeHypermutatedSequences.R script by setting environment variables. Information was passed back to the identify-founders.pl script by printing to STDOUT and by saving results in a file whose name is specified by one of the environment variables.

To ease integration of hypermutR into the hiv-founder-id pipeline, a removeHypermutatedSequences.R script is included in the inst folder of the package. This script can be called using the call that was originally included in the identify-founders.pl script. To locate this script after you installed hypermutR, run the command print(file.path(find.package('hypermutR'), 'removeHypermutatedSequences.R')) from within an R session. To modify the identify-founders.pl script to use hypermutR, you can just replace the removeHypermutatedSequences.R script in the founder pipleline folder with the removeHypermutatedSequences.R script from the hypermutR package.

The intended way to use hypermutR is either via the hypermutR.R script included in the package's inst directory or by importing the package in an R session and calling the remove_hypermut function. The removeHypermutatedSequences.R script is just provided to make integration into the founder-pipeline more convenient.

Interface details of removeHypermutatedSequences.R

Environment variables set by identify-founders.pl when calling removeHypermutatedSequences.R:

• removeHypermutatedSequences_fixWith
• removeHypermutatedSequences_fixInsteadOfRemove
• removeHypermutatedSequences_pValueThreshold
• removeHypermutatedSequences_inputFilename
• removeHypermutatedSequences_outputDir

Output expected by identify-founders.pl from removeHypermutatedSequences.R.

• Number of hypermutated sequences printed to STDOUT.
• Fasta file written out by ape::write.dna to removeHypermutatedSequences_outputDir/removeHypermutatedSequences_inputFilename with the call write.dna( out.fasta, out.fasta.file, format = "fasta", colsep = "", indent = 0, blocksep = 0, colw = 72 )

philliplab/hypermutR documentation built on Sept. 2, 2020, 2:51 p.m.