An Unified Interface to Extract Signatures

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.

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

# \donttest{
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"
)
#> NMF algorithm: 'brunet'
#> NMF seeding method: random
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#> DONE (converged at 470/2000 iterations)
# Auto-extract signatures based on bayesian NMF
res2 <- sig_unify_extract(cn_tally_W$nmf_matrix,
  nrun = 1,
  approach = "bayes_nmf"
)
#> Set 5 as the initial signature number
#> Select Run 1, which K = 2 as best solution.
# }