signatures: Retrieve signatures from a result_model, result_collection,...

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Retrieve signatures from a result_model, result_collection, or musica object

Description

The signatures matrix contains the probability of mutation motif in each sample. Rows correspond to each motif and columns correspond to each signature.

Usage

signatures(x, ...)

## S4 method for signature 'musica'
signatures(x, result, modality, model_id)

## S4 method for signature 'result_collection'
signatures(x, modality, model_id)

## S4 method for signature 'result_model'
signatures(x)

signatures(x, ...) <- value

## S4 replacement method for signature 'musica,matrix'
signatures(x, result, modality, model_id) <- value

## S4 replacement method for signature 'result_collection,matrix'
signatures(x, modality, model_id) <- value

## S4 replacement method for signature 'result_model,matrix'
signatures(x) <- value

Arguments

x	A musica, result_collection, or result_model object generated by a mutational discovery or prediction tool.
...	Other inputs
result	Name of result from result_list to assign the signatures. Used when result is a musica object.
modality	Modality to assign the signatures. Used when result is a musica or result_collection object.
model_id	Model identifier to assign the signatures. Used when result is a musica or result_collection object.
value	A matrix of motifs counts by samples

Value

A matrix of mutational signatures

Examples

data(res)
signatures(res, "result", "SBS96", "res")
data(res)
signatures(res, "result", "SBS96", "res") <- matrix()

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