extractSig: Infer Signature Proportions

In mskcc/tempoSig: Maximum Likelihood Fitting of Mutational Catalogs and De Novo Inference of Signatures

Infer Signature Proportions

Description

Use known signature list to find the most likely exposures in samples

Usage

extractSig(
  object,
  method = "mle",
  itmax = 1000,
  tol = 1e-04,
  min.tmb = 2,
  compute.pval = FALSE,
  nperm = 1000,
  progress.bar = FALSE,
  pvtest = "permutation",
  cosmic = FALSE,
  Kmin = 2,
  K = 2,
  Kmax = 30,
  nrun = 10,
  useC = TRUE,
  initializer = "random",
  verbose = 2,
  ...
)

Arguments

object	Object of class tempoSig
method	Refitting method; mle for maximum likelihood (default) or mutCone for mutationalCone.
itmax	Maximum number of iterations for maximum likelihood estimate
tol	Tolerance for convergence
min.tmb	Minimum number of mutations in each sample. If tmb is less, NA will be returned for the sample.
compute.pval	Estimate p-values
nperm	Number of permutations
progress.bar	Display progress bar
pvtest	Algorithm for p-value computation; c('permutation','lrt','x.permutation') for permutation resampling of signatures, likelihood ratio test (asymptotic formula), or permutation of count data.
...	Other parameters for denovo with method = 'hnmf'

Examples

data <- read.table(system.file('extdata', 'tcga-brca_catalog.txt', package='tempoSig'))
b <- tempoSig(data)
b <- extractSig(b, progress.bar = TRUE)
b_pv <- extractSig(b, compute.pval = TRUE, progress.bar = TRUE)

mskcc/tempoSig documentation built on Feb. 3, 2023, 8:35 a.m.