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,
  modality,
  signature_res,
  algorithm,
  min_exists = 0.05,
  proportion_samples = 0.25,
  rare_exposure = 0.4,
  result_name = "result",
  model_id = NULL
)

Arguments

musica	A musica object.
modality	Modality 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" and decompTumor2Sig
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
result_name	Name for result_list entry to save the results to. Default "result".
model_id	Identifier for the result. If NULL, will be automatically set to the algorithm and number of signatures. Default NULL.

Value

Returns new musica object with the results.

campbio/musicatk documentation built on Dec. 25, 2024, 9:34 p.m.