cnv_derivefeatures: Derive copy number feature distributions
In ShixiangWang/VSHunter: Capture Variation Signatures from Genomic Data

Description Usage Arguments Value Author(s) See Also Examples

This function summarise each copy-number profile using a number of different feature distributions: sigment size, breakpoint number (per ten megabase), change-point copy-number, segment copy-number, breakpoint number (per chromosome arm), length of segments with oscilating copy-number.

1 2	cnv_derivefeatures(CN_data, cores = 1, genome_build = c("hg19", "hg38"))

`CN_data`	a `QDNAseqCopyNumbers` object or a `list` contains multiple `data.frame`s (recommended), each `data.frame` stores copy-number profile for one sample with 'chromosome', 'start', 'end' and 'segVal' these four necessary columns. Of note, 'segVal' column shoule be absolute copy number values.
`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.
`genome_build`	genome build version, must be one of 'hg19' or 'hg38'.

a list contains six copy number feature distributions.

Geoffrey Macintyre, Shixiang Wang

cnv_plotFeatureDistribution() for plotting feature distributions.

Other CNV analysis functions: cnv_autoCaptureSignatures, cnv_chooseSigNumber, cnv_extractSignatures, 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")

## End(Not run)