Derive copy number feature distributions

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

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

Arguments

CN_data	a QDNAseqCopyNumbers object or a list contains multiple data.frames each one 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 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'.

Value

a list contains six copy number feature distributions.

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 = cnv_derivefeatures(CN_data = tcga_segTabs, cores = 1, genome_build = "hg19")
# }