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Automatic filtering of inactive signatures

Source: R/discovery_prediction.R
auto_subset_sigs.Rd

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.