get_signature: Function to obtain a SuperSig

In TomasettiLab/supersigs: Supervised mutational signatures

Description

Generate a tissue-specific SuperSig for a given dataset of mutations and exposure factor. Returns the SuperSig and a classification model trained with the SuperSig.

Usage

get_signature(data, factor, wgs = FALSE)

Arguments

data	a data frame of mutations containing columns for sample_id, age, IndVar, and the 96 trinucleotide mutations (see vignette for details)
factor	the factor/exposure (e.g. "age", "smoking"). If the factor = "age", the SuperSig is computed using counts. Otherwise, rates (counts/age) are used.
wgs	logical value indicating whether sequencing data is whole-genome (wgs = TRUE) or whole-exome (wgs = FALSE)

Value

get_signature returns an object of class SuperSig

Examples

head(example_dt) # use example data from package
input_dt <- make_matrix(example_dt) # convert to correct format
input_dt$IndVar <- c(1, 1, 1, 0, 0) # add IndVar column
get_signature(data = input_dt, factor = "Age") # get SuperSig

TomasettiLab/supersigs documentation built on Dec. 13, 2021, 12:53 a.m.