icgc_curate: Sorts and removes duplicate entries in a mutation file output...

In antoine186/convSig: Mutational Process Inference via Expectation Maximisation

Description

Sorts and removes duplicate entries in a mutation file output by icgc2mut()

Usage

icgc_curate(mut_file, remove.nonSNP = TRUE)

Arguments

mut_file	A mutation file output by icgc2mut().
remove.nonSNP	A boolean variable indicating whether the function should remove non-single nucleotide changes. This is set by default to TRUE as our downstream filtering method only handles single nucleotide changes.

Value

A sorted mutation file with duplicate entries removed and, depending on user specification, non-single nucleotide changes removed.

Details

Your input mutation file must at least have the following column headers: icgc_sample_id (i.e. the ICGC sample ID), chromosome (i.e. the Chromosome ID), chromosome_start (i.e. the chromosome start position), chromosome_end (i.e. the chromosome end position), mutated_from_allele (i.e. the reference allele), and mutated_to_allele (i.e. alternate allele).

Examples

res <- icgc_curate(mutation_data)

antoine186/convSig documentation built on Jan. 17, 2020, 4:09 a.m.