sigminer (version 0.1.11)

get_LengthFraction: Calculate length fraction profile of copy number

Description

Calculate length fraction profile of copy number

Usage

get_LengthFraction(CN_data, genome_build = c("hg19", "hg38"),
  seg_cols = c("Chromosome", "Start.bp", "End.bp", "modal_cn"),
  samp_col = "sample")

Arguments

CN_data

a data.frame with 'chromosome', 'start', 'end' and 'segVal' (optinal) and 'sample' these five columns (specify column names using seg_cols and samp_cols options) or a list contains multiple data.frames, each data.frame stores copy-number profile for one sample with 'chromosome', 'start', 'end' and 'segVal' (optional) these four columns. If 'sample' column is not specified, will try using name of each data.frame.

genome_build

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

seg_cols

four characters used to specify chromosome, start position, end position and copy number value in input, respectively. Default use names from ABSOLUTE calling result.

samp_col

a character used to specify the sample column name.

Value

a data table

See Also

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

Examples

# NOT RUN {
# Load copy number list
load(system.file("extdata", "toy_cnlist.RData",
  package = "sigminer", mustWork = TRUE
))
annot <- get_LengthFraction(cn_list, seg_cols = c("chromosome", "start", "end", "segVal"))
# }