sig_unify_extract: An Unified Interface to Extract Signatures

In sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

An Unified Interface to Extract Signatures

Description

This function provides an unified interface to signature extractor implemented in sigminer. If you determine a specific approach, please also read the documentation of corresponding extractor. See "Arguments" part.

Usage

sig_unify_extract(
  nmf_matrix,
  range = 2:5,
  nrun = 10,
  approach = c("bayes_nmf", "repeated_nmf", "bootstrap_nmf", "sigprofiler"),
  cores = 1L,
  ...
)

Arguments

nmf_matrix	a matrix used for NMF decomposition with rows indicate samples and columns indicate components.
range	signature number range, i.e. 2:5.
nrun	the number of iteration to be performed to extract each signature number.
approach	approach name. "repeated_nmf" - sig_extract "bayes_nmf" - sig_auto_extract "bootstrap_nmf" - bp_extract_signatures "sigprofiler" - sigprofiler
cores	number of cores used for computation.
...	other parameters passing to signature extractor based on the approach setting.

Value

Result dependent on the approach setting.

See Also

sig_extract, sig_auto_extract, bp_extract_signatures, sigprofiler

Examples

load(system.file("extdata", "toy_copynumber_tally_W.RData",
  package = "sigminer", mustWork = TRUE
))
# Extract signatures
# It is same as sig_extract(cn_tally_W$nmf_matrix, 2, nrun = 1)
res <- sig_unify_extract(cn_tally_W$nmf_matrix, 2,
  nrun = 1,
  approach = "repeated_nmf"
)
# Auto-extract signatures based on bayesian NMF
res2 <- sig_unify_extract(cn_tally_W$nmf_matrix,
  nrun = 1,
  approach = "bayes_nmf"
)

sigminer documentation built on Aug. 21, 2023, 9:08 a.m.