generate_result_grid: Generate result_grid from musica based on annotation and...

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Generate result_grid from musica based on annotation and range of k

Description

Generate result_grid from musica based on annotation and range of k

Usage

generate_result_grid(
  musica,
  table_name,
  algorithm = "lda",
  annotation = NA,
  k_start,
  k_end,
  n_start = 1,
  seed = NULL,
  par_cores = FALSE,
  verbose = FALSE
)

Arguments

musica	A musica object.
table_name	Name of table used for signature discovery
algorithm	Algorithm for signature discovery
annotation	Sample annotation to split results into
k_start	Lower range of number of signatures for discovery
k_end	Upper range of number of signatures for discovery
n_start	Number of times to discover signatures and compare based on posterior loglikihood
seed	Seed to use for reproducible results, set to null to disable
par_cores	Number of parallel cores to use (NMF only)
verbose	Whether to output loop iterations

Value

A result object containing signatures and sample weights

Examples

data(musica_sbs96)
grid <- generate_result_grid(musica_sbs96, "SBS96", "lda", k_start = 2, 
k_end = 5)

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