predict_exposure: Prediction of exposures in new samples using pre-existing...

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Prediction of exposures in new samples using pre-existing signatures

Description

Exposures for samples will be predicted using an existing set of signatures stored in a result_model object. Algorithms available for prediction include a modify version of "lda", and "decompTumor2Sig".

Usage

predict_exposure(
  musica,
  modality,
  signature_res,
  algorithm = c("lda", "decompTumor2Sig"),
  result_name = "result",
  model_id = NULL,
  signatures_to_use = seq_len(ncol(signatures(signature_res))),
  verbose = FALSE,
  make_copy = FALSE,
  table_name = NULL
)

Arguments

musica	A musica object.
modality	Modality for posterior prediction. Must match the table type used to generate the prediction signatures
signature_res	Signatures used to predict exposures for the samples musica object. Existing signatures need to stored in a result_model object.
algorithm	Algorithm to use for prediction of exposures. One of "lda" or "decompTumor2Sig".
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.
signatures_to_use	Which signatures in the signature_res result object to use. Default is to use all signatures.
verbose	If TRUE, progress will be printing. Only used if algorithm = "lda". Default FALSE.
make_copy	If FALSE, the inputted musica object is updated and nothing is returned. If TRUE, a new musica object is created and returned. Default FALSE.
table_name	Use modality instead

Value

Returns nothing or a new musica object, depending on the make_copy parameter.

Examples

data(musica)
data(cosmic_v2_sigs)
g <- select_genome("19")
build_standard_table(musica, g, "SBS96", overwrite = TRUE)
result <- predict_exposure(
  musica = musica, modality = "SBS96",
  signature_res = cosmic_v2_sigs, algorithm = "lda"
)

# Predict using LDA-like algorithm with seed set to 1
set.seed(1)
predict_exposure(
  musica = musica, modality = "SBS96",
  signature_res = cosmic_v2_sigs, algorithm = "lda"
)

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