getTriContextFraction: Calculates trinucleotide context fraction

In deconstructSigs: Identifies Signatures Present in a Tumor Sample

Description

Determines trinucleotide context fraction from a mutation counts list. Given a data frame or .txt file or mutation counts with columns as trincucleotide contexts in the form A[C>A]A and the rows as sample id's and a data frame or .txt file of the times each tri nucleotide context is seen in the sequencing region with the rows in the format ACA, the function returns a data frame of the mutation counts normalized by trinucleotide frequency

Usage

getTriContextFraction(mut.counts.ref, trimer.counts.method)

Arguments

mut.counts.ref	data frame of counts of mutations in each trinucleotide context for each sample or location where .txt file is found
trimer.counts.ref	data frame of counts of times each trinculeotide context is seen in sequencing area or location where the .txt file is found

Value

Returns the trinucleotide context fraction

deconstructSigs documentation built on May 2, 2019, 4:06 a.m.