auto_subset_sigs: Automatic filtering of inactive signatures

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Automatic filtering of inactive signatures

Description

Automatic filtering of inactive signatures

Usage

auto_subset_sigs(
  musica,
  table_name,
  signature_res,
  algorithm,
  min_exists = 0.05,
  proportion_samples = 0.25,
  rare_exposure = 0.4
)

Arguments

musica	A musica object.
table_name	Name of table used for posterior prediction (e.g. SBS96)
signature_res	Signatures to automatically subset from for prediction
algorithm	Algorithm to use for prediction. Choose from "lda_posterior", decompTumor2Sig, and deconstructSigs
min_exists	Threshold to consider a signature active in a sample
proportion_samples	Threshold of samples to consider a signature active in the cohort
rare_exposure	A sample will be considered active in the cohort if at least one sample has more than this threshold proportion

Value

A result object containing automatically subset signatures and corresponding sample weights

campbio/musicatk documentation built on Oct. 22, 2023, 8:28 p.m.