Extract signature based on specified rank value

Extract signature based on specified rank value

cnv_extractSignatures(sample_by_component, nsig, seed = 123456,
  nmfalg = "brunet", cores = 1)

Arguments

sample_by_component	a sample-by-component matrix, generate from cnv_generateSbCMatrix function.
nsig	specification of the factorization rank.
seed	seed number.
nmfalg	specification of the NMF algorithm.
cores	number of compute cores to run this task. You can use detectCores function to check how many cores you can use. If you are using cnv_pipe feature, please do not use maximal number of cores in your computer, it may cause some unexpected problems.

Value

a object of NMF run.

Examples

# NOT RUN {
## load example copy-number data from tcga
load(system.file("inst/extdata", "example_cn_list.RData", package = "VSHunter"))
## generate copy-number features
tcga_features = cnv_derivefeatures(CN_data = tcga_segTabs, cores = 1, genome_build = "hg19")
## fit mixture model  (this will take some time)
tcga_components = cnv_fitMixModels(CN_features = tcga_features, cores = 1)
## generate a sample-by-component matrix
tcga_sample_component_matrix = cnv_generateSbCMatrix(tcga_features, tcga_components, cores = 1)
## optimal rank survey
 tcga_sig_choose = cnv_chooseSigNumber(tcga_sample_component_matrix, nrun = 10,
 cores = 1, plot = FALSE)
 tcga_signatures = cnv_extractSignatures(tcga_sample_component_matrix, nsig = 3, cores = 1)
# }