Generate a sample-by-component matrix

This function generate a sample-by-component matrix representing the sum of posterior probabilities of each copy-number event being assigned to each component.

generate_sbcMatrix(CN_features, all_components = NULL, cores = 1,
  rowIter = 1000)

Arguments

CN_features	a list contains six copy number feature distributions, obtain this from derive_features function.
all_components	a list contain flexmix object of copy-number features, obtain this from fit_mixModels function or use pre-compiled components data which come from CNV signature paper https://www.nature.com/articles/s41588-018-0179-8 (set this argument as NULL).
cores	number of compute cores to run this task.
rowIter	step size of iteration for rows of ech CNV feature data.frame.

Value

a numeric sample-by-component matrix

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 = derive_features(CN_data = tcga_segTabs, cores = 1, genome_build = "hg19")
## fit mixture model  (this will take some time)
tcga_components = fit_mixModels(CN_features = tcga_features, cores = 1)
## generate a sample-by-component matrix
tcga_sample_component_matrix = generate_sbcMatrix(tcga_features, tcga_components, cores = 1)
# }