auto_subset_sigs: Automatic filtering of inactive signatures

In campbio/BAGEL: Novel Mutational Signature Analysis

Description

Automatic filtering of inactive signatures

Usage

auto_subset_sigs(
  bagel,
  table_name,
  signature_res,
  algorithm,
  min_exists = 0.05,
  proportion_samples = 0.25,
  rare_exposure = 0.4,
  seed = 1
)

Arguments

bagel	Input samples to predit signature weights
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
seed	Seed to use for reproducible results, set to null to disable

Value

Results a result object containing automatically subset signatures and corresponding sample weights

campbio/BAGEL documentation built on Oct. 6, 2020, 3:59 a.m.