mut_count: Computes the frequency of each possible trinucleotide or...

In antoine186/convSig: Mutational Process Inference via Expectation Maximisation

Description

Computes the frequency of each possible trinucleotide or 5-nucleotide mutation signature

Usage

mut_count(reference, mut_file, five = FALSE, slice = FALSE)

Arguments

reference	The path leading to your assembly file (.fa or .fa.gz).
mut_file	The path leading to your mutation input file (tsv or csv only). Alternatively, this is your mutation data if you supplied either a data.frame or a matrix. Please make sure that your input data is not malformed; It should contain the following columns: icgc_sample_id (i.e. the ICGC sample ID), chromosome (i.e. the Chromosome ID), chromosome_start (i.e. the chromosome start position), mutated_from_allele (i.e. the reference allele), and mutated_to_allele (i.e. alternate allele).
five	A boolean variable. A value of TRUE will lead to the function scanning the input files for 5 bases mutation signatures as opposed to 3 bases signatures. a value of FALSE causes the function to scan for 3 bases signatures.
slice	A boolean variable. A value of TRUE will slice the assembly provided and only keep the chromosomes that appear in your mutation input file.

Value

A background mutation signatures vector (wt), which provides the frequency of each possible signature given an assembly file. A matrix (mut_mat) containing the mutational rate of each signature for each sample in your supplied mutation input file.

Examples

assembly <- "Homo_sapiens.GRCh37.dna.primary_assembly.fa"
mut_file <- "mutation_file_input.tsv"

mut_sign <- mut_count(assembly, mut_file)

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