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,
  modality,
  algorithm = "lda",
  annotation = NA,
  k_start,
  k_end,
  result_name = "result_grid",
  n_start = 1,
  seed = NULL,
  par_cores = FALSE,
  verbose = FALSE,
  make_copy = FALSE,
  table_name = NULL
)

Arguments

musica	A musica object.
modality	Modality 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
result_name	Name for result_list entry to save the results to. Default "result_grid".
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
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_sbs96)
grid <- generate_result_grid(musica_sbs96, "SBS96", "lda",
  k_start = 2,
  k_end = 5
)

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