combine_predict_grid: Combine prediction grid list into a result object. Exposure...

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Combine prediction grid list into a result object. Exposure values are zero for samples in an annotation where that signature was not predicted

Description

Combine prediction grid list into a result object. Exposure values are zero for samples in an annotation where that signature was not predicted

Usage

combine_predict_grid(grid_list, musica, table_name, signature_res)

Arguments

grid_list	A list of result objects from the prediction grid to combine into a single result
musica	A musica object.
table_name	Table name used for prediction
signature_res	Signatures to automatically subset from for prediction

Value

A result object combining all samples and signatures from a prediction grid. Samples have zero exposure value for signatures not found in that annotation type.

Examples

data(musica_annot)
data(cosmic_v2_sigs)
grid <- auto_predict_grid(musica_annot, "SBS96", cosmic_v2_sigs, "lda",
"Tumor_Subtypes", combine_res = FALSE)
combined <- combine_predict_grid(grid, musica_annot, "SBS96", cosmic_v2_sigs)
plot_exposures(combined, group_by = "annotation", 
annotation="Tumor_Subtypes")

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