auto_subset_sigs: Automatic filtering of inactive signatures

View source: R/discovery_prediction.R

auto_subset_sigsR Documentation

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" 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

Value

A result object containing automatically subset signatures and corresponding sample weights


campbio/musicatk documentation built on July 14, 2024, 8:28 a.m.