cnv_generateSbCMatrix: Generate a sample-by-component matrix
In ShixiangWang/VSHunter: Capture Variation Signatures from Genomic Data

Description Usage Arguments Value Author(s) See Also Examples

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

1 2	cnv_generateSbCMatrix(CN_features, all_components = NULL, cores = 1, rowIter = 1000)

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

a numeric sample-by-component matrix

Geoffrey Macintyre, Shixiang Wang

Other CNV analysis functions: cnv_autoCaptureSignatures, cnv_chooseSigNumber, cnv_derivefeatures, cnv_extractSignatures, cnv_fitMixModels, cnv_getLengthFraction, cnv_pipe, cnv_plotDistributionProfile, cnv_plotFeatureDistribution, cnv_plotMixComponents, cnv_plotSignatures, cnv_quantifySigExposure, cnv_readprofile

## 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)

## End(Not run)