mutationSpectrum: Mutation spectrum analyses

In h5vc: Managing alignment tallies using a hdf5 backend

Description

These functions help in analyses of mutation spectra

Usage

mutationSpectrum( variantCalls, tallyFile, study, context = 1 )

Arguments

variantCalls	A data.frame object that can be the output of a call to a callVariantsPaired or callDeletionsPaired function. The following columns are required: - altAllele - refAllele - Sample - Start - End - Chrom
tallyFile	filename of a tally file matching the variant calls
study	the study id used in the tally file
context	An integer specifying the size of the context that should be considered (i.e. the length of the prefix and suffix of the variant call)

Details

This function takes a set of variant calls (SNVs/Deletions) and a tallyFile as well as a context size and tabulates the number of observed mutations stratified by type (refAllele->altAllele) and sequence context (i.e. the prefix and suffix of size context around the variant position in the genome)

bases serves to map character representations to numeric encoding of bases

variantCalls is an example dataset of variant calls created by running callVariantsPaired on the example.tally.hfs5 file.

Value

A table listing the counts of mutations stratified by allele, sequence context and sample.

Author(s)

Paul Pyl

Examples

  library(h5vc)
  tallyFile <- system.file( "extdata", "example.tally.hfs5", package = "h5vcData" )
  data( "example.variants", package = "h5vcData" )
  head( mutationSpectrum( variantCalls, tallyFile, "/ExampleStudy" ) )

h5vc documentation built on Nov. 8, 2020, 4:56 p.m.