cnv_extractSignatures: Extract signature based on specified rank value
In ShixiangWang/VSHunter: Capture Variation Signatures from Genomic Data

Description Usage Arguments Value Author(s) See Also Examples

Extract signature based on specified rank value

1 2	cnv_extractSignatures(sample_by_component, nsig, seed = 123456, nmfalg = "brunet", cores = 1)

`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 `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.

a object of NMF run.

Geoffrey Macintyre, Shixiang Wang

cnv_plotSignatures() for plot signatures and their contributions.

Other CNV analysis functions: cnv_autoCaptureSignatures, cnv_chooseSigNumber, cnv_derivefeatures, cnv_fitMixModels, cnv_generateSbCMatrix, 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)
## 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)

## End(Not run)