get_cn_freq_table {sigminer}

Get CNV Frequency Table

Description

Get CNV Frequency Table

Usage

get_cn_freq_table(
  data,
  genome_build = "hg19",
  cutoff = 2L,
  resolution_factor = 1L
)

Arguments

data

a CopyNumber object or a data.frame containing at least 'chromosome', 'start', 'end', 'segVal', 'sample' these columns.

genome_build

genome build version, used when data is a data.frame, should be 'hg19' or 'hg38'.

cutoff

copy number value cutoff for splitting data into AMP and DEL. The values equal to cutoff are discarded. Default is 2, you can also set a length-2 vector, e.g. c(2, 2).

resolution_factor

an integer to control the resolution. When it is 1 (default), compute frequency in each cytoband. When it is 2, use compute frequency in each half cytoband.

Value

a data.table.