cnv_quantifySigExposure: Quantify exposure for samples using Linear Combination...
In ShixiangWang/VSHunter: Capture Variation Signatures from Genomic Data

Description Usage Arguments Value Author(s) See Also Examples

Quantify exposure for samples using Linear Combination Decomposition (LCD)

1 2	cnv_quantifySigExposure(sample_by_component, component_by_signature = NULL)

`sample_by_component`	a sample-by-component `matrix`, generate from cnv_generateSbCMatrix function.
`component_by_signature`	a componet by signature matrix, default is `NULL`, it will use pre-compiled data from CNV signature paper https://www.nature.com/articles/s41588-018-0179-8.

a list contains absolute/relative exposure.

Geoffrey Macintyre, Shixiang Wang

Other CNV analysis functions: cnv_autoCaptureSignatures, cnv_chooseSigNumber, cnv_derivefeatures, cnv_extractSignatures, cnv_fitMixModels, cnv_generateSbCMatrix, cnv_getLengthFraction, cnv_pipe, cnv_plotDistributionProfile, cnv_plotFeatureDistribution, cnv_plotMixComponents, cnv_plotSignatures, 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)
 w = NMF::basis(tcga_signatures) # signature matrix
 tcga_exposure = cnv_quantifySigExposure(sample_by_component =
 tcga_sample_component_matrix, component_by_signature = w)

## End(Not run)