discover_signatures: Discovers signatures and weights from a table of counts using...

In campbio/BAGEL: Novel Mutational Signature Analysis

Description

Discovers signatures and weights from a table of counts using NMF

Usage

discover_signatures(
  bagel,
  table_name = NULL,
  num_signatures,
  method = "lda",
  seed = 1,
  nstart = 1,
  par_cores = FALSE
)

Arguments

bagel	A bagel object or counts table
table_name	Name of table used for signature discovery
num_signatures	Number of signatures to discover, k
method	Discovery of new signatures using either LDA or NMF
seed	Seed for reproducible signature discovery
nstart	Number of independent runs with optimal chosen (lda only)
par_cores	Number of parallel cores to use (NMF only)

Value

Returns a result object with results and input object (if bagel)

Examples

bay <- readRDS(system.file("testdata", "bagel.rds", package = "BAGEL"))
g <- select_genome("19")
build_standard_table(bay, g, "SBS96", overwrite = TRUE)
discover_signatures(bagel = bay, table_name = "SBS96",
num_signatures = 3, method = "nmf", seed = 12345, nstart = 1)

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