generate_result_grid: Generate result_grid from bagel based on annotation and range...

In campbio/BAGEL: Novel Mutational Signature Analysis

Description

Generate result_grid from bagel based on annotation and range of k

Usage

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

Arguments

bagel	Input bagel to generate grid from
table_name	Name of table used for signature discovery
discovery_type	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

Results a result object containing signatures and sample weights

Examples

bay <- readRDS(system.file("testdata", "bagel_sbs96.rds", package = "BAGEL"))
grid <- generate_result_grid(bay, "SBS96", "nmf", k_start = 2, k_end = 5)

campbio/BAGEL documentation built on Oct. 6, 2020, 3:59 a.m.