sigminer (version 0.1.11)

prepare_copynumber: Prepare nmf input matrix for copy number signature analysis

Description

Prepare nmf input matrix for copy number signature analysis

Usage

prepare_copynumber(CopyNumber, reference_components = FALSE, cores = 1,
  seed = 123456, min_comp = 2, max_comp = 10, min_prior = 0.001,
  model_selection = "BIC", nrep = 1, niter = 1000, rowIter = 1000)

Arguments

CopyNumber

a CopyNumber object.

reference_components

default is FALSE, calculate mixture components from CopyNumber object. If set it to NULL, use pre-compiled components data which come from CNV signature paper. If can also be a list contain flexmix object of copy-number features, obtain this from get_components function.

cores

number of compute cores to run this task. You can use parallel::detectCores() function to check how many cores you can use.

seed

seed number.

min_comp

minimal number of components to fit, default is 2. Can also be a vector with length 6, which apply to each feature.

max_comp

maximal number of components to fit, default is 10. Can also be a vector with length 6, which apply to each feature.

min_prior

minimal prior value, default is 0.001. Details about custom setting please refer to flexmix package.

model_selection

model selection strategy, default is 'BIC'. Details about custom setting please refer to flexmix package.

nrep

number of run times for each value of component, keep only the solution with maximum likelihood.

niter

maximal number of iteration to achive converge.

rowIter

step size of iteration for rows of ech CNV feature.

Value

a list contains matrix for NMF input, copy number features and components.

See Also

Other signature analysis prepare function series: prepare_maf

Examples

# NOT RUN {
# Load copy number object
load(system.file("extdata", "toy_copynumber.RData",
  package = "sigminer", mustWork = TRUE
))
cn_prepare <- prepare_copynumber(cn)
# }