sigminer (version 0.1.11)

get_cnsummary_sample: Get summary of copy number variation per sample

Description

Include number of CNV segments, CNA burden, number of CNV amplification segments, number of CNV deletion segments etc..

Usage

get_cnsummary_sample(segTab, genome_build = c("hg19", "hg38"),
  genome_measure = c("called", "wg"), min_seg_len = 1000L)

Arguments

segTab

a data.frame with 'chromosome', 'start', 'end' and 'segVal' and 'sample' these five ordered columns. 'chromosome' should have prefix "chr".

genome_build

genome build version, should be 'hg19' or 'hg38'.

genome_measure

default is 'called', can be 'wg' or 'called'. Set 'called' will use autosomo called segments size to compute total size for CNA burden calculation, this option is useful for WES and target sequencing. Set 'wg' will use autosome size from genome build, this option is useful for WGS, SNP etc..

min_seg_len

minimal length of CNV segment for CNA burden calculation, default is 1000. (!NOT implement NOW!)

Value

a data table

Details

CNA burden, a simple metric of CNA level defined as the percent of the autosomal tumor genome bearing CNAs, could be used as an informative measure of CNA.

References

Hieronymus, Haley, et al. "Copy number alteration burden predicts prostate cancer relapse." Proceedings of the National Academy of Sciences 111.30 (2014): 11139-11144.

See Also

Other internal calculation function series: get_ArmLocation, get_LengthFraction, get_cnlist, get_components, get_features, get_matrix

Examples

# NOT RUN {
load(system.file("extdata", "example_cn_list.RData",
  package = "sigminer", mustWork = TRUE
))
segTabs <- data.table::rbindlist(tcga_segTabs, idcol = "sample")
segTabs$chromosome <- paste0("chr", segTabs$chromosome)
samp_sum <- get_cnsummary_sample(segTabs[, c(2:5, 1)])
# }