Choose optimal number of signatures

This function use NMF package to evaluate the optimal number of signatures. The most

cnv_chooseSigNumber(sample_by_component, nTry = 12, nrun = 10,
  cores = 1, seed = 123456, plot = TRUE, testRandom = TRUE)

Arguments

sample_by_component	a sample-by-component matrix, generate from cnv_generateSbCMatrix function.
nTry	the maximal tried number of signatures, default is 12. Of note, this value should far less than number of features or samples.
nrun	the number of run to perform for each value in range of 2 to nTry, default is 10. According to NMF package documentation, nrun set to 50 is enough to achieve robust result.
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.
seed	seed number.
plot	logical. If TRUE, plot best rank survey.
testRandom	if generate random data from input to test measurements. Default is TRUE.

Value

a list contains information of NMF run and rank survey.

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)
# }