sigminer (version 1.0.6)

sig_extract: Extract Signatures through NMF

Description

Do NMF de-composition and then extract signatures.

Usage

sig_extract(
  nmf_matrix,
  n_sig,
  nrun = 10,
  cores = 1,
  method = "brunet",
  optimize = FALSE,
  pConstant = NULL,
  seed = 123456,
  ...
)

Arguments

nmf_matrix

a matrix used for NMF decomposition with rows indicate samples and columns indicate components.

n_sig

number of signature. Please run sig_estimate to select a suitable value.

nrun

a numeric giving the number of run to perform for each value in range, nrun set to 30~50 is enough to achieve robust result.

cores

number of cpu cores to run NMF.

method

specification of the NMF algorithm. Use 'brunet' as default. Available methods for nmf decompositions are 'brunet', 'lee', 'ls-nmf', 'nsNMF', 'offset'.

optimize

logical, for exposure optimization, especially useful for copy number signature.

pConstant

A small positive value (like 1e-9) to add to the matrix. Use it ONLY if the functions throws an non-conformable arrays error.

seed

specification of the starting point or seeding method, which will compute a starting point, usually using data from the target matrix in order to provide a good guess.

...

other arguments passed to NMF::nmf().

Value

a list with Signature class.

References

Gaujoux, Renaud, and Cathal Seoighe. "A flexible R package for nonnegative matrix factorization." BMC bioinformatics 11.1 (2010): 367.

Mayakonda, Anand, et al. "Maftools: efficient and comprehensive analysis of somatic variants in cancer." Genome research 28.11 (2018): 1747-1756.

See Also

sig_tally for getting variation matrix, sig_estimate for estimating signature number for sig_extract, sig_auto_extract for extracting signatures using automatic relevance determination technique.

Examples

# NOT RUN {
load(system.file("extdata", "toy_copynumber_tally_M.RData",
  package = "sigminer", mustWork = TRUE
))
# Extract copy number signatures
library(NMF)
res <- sig_extract(cn_tally_M$nmf_matrix, 2, nrun = 1)
# }