vcf2mut: Read vcf files and processes them / User correct assembly

In antoine186/convSig: Mutational Process Inference via Expectation Maximisation

Description

Read vcf files and processes them / User correct assembly

Usage

vcf2mut(datapath, geno = "GT", assembly, five = FALSE)

Arguments

datapath	The path leading to your multisampled vcf file.
geno	An ID Format string in your vcf file indicating the index of the genotype information.
assembly	The path leading to your assembly file (.fa or .fa.gz).
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.

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 <- "multisampled_mutations.vcf"

mut_sign <- vcf2mut(mut_file, "GT", assembly)

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