loadCopyNumberCallsDNAcopy: loadCopyNumberCallsDNAcopy

In bernatgel/CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality

loadCopyNumberCallsDNAcopy

Description

Loads copy number calls from DNACopy results.

Usage

loadCopyNumberCallsDNAcopy(DNAcopy.data, chr.col = "chrom", start.col = "loc.start", end.col = "loc.end", segment.value.col = "seg.mean", cn.col = NULL, chr.transformation = "23:X,24:Y,25:MT", genome = NULL, verbose = TRUE)

Arguments

DNAcopy.data	The name of the file with the data
chr.col	(number or character) The name or number of the column with chromosome information. If NULL, it is automatically identified. (defaults to "chrom")
start.col	(number or character) The name or number of the column with start position information. If NULL, it is automatically identified. (defaults to "loc.start")
end.col	(number or character) The name or number of the column with end position information. If NULL, it is automatically identified. (defaults to "loc.end")
segment.value.col	(number or character) The name or number of the column with segment value. If NULL, it is automatically identified. (defaults to "seg.mean")
cn.col	(number or character) The name or number of the column with CN information. If NULL, it is automatically identified. (defaults to NULL)
chr.transformation	(character) The transformation of the chromosome names in a comma separated "key:value" format.(defaults to "23:X,24:Y,25:MT")
genome	(character) The name of the genome (defaults to NULL)
verbose	(logical) Whether to show information messages. (defaults to TRUE)

Details

This function will load segments data from DNAcopy data structure in R. Internally it uses the toGRanges function from regioneR package and can work with any format accepted by it, including R objects and local or remote files. If no column names are specified, it will use simple heuristics to try to identify the relevant data columns.

Value

A GRanges with a range per copy number segment or a list of GRanges with a GRanges per sample.

Examples

library(DNAcopy)

data(coriell)
CNA.object <- suppressWarnings(CNA(cbind(coriell$Coriell.05296), coriell$Chromosome, coriell$Position, data.type="logratio",sampleid="c05296"))

smoothed.CNA.object <- smooth.CNA(CNA.object)
DNAcopy.data <- segment(smoothed.CNA.object, verbose=1)

cnv.call <- loadCopyNumberCallsDNAcopy(DNAcopy.data = DNAcopy.data)

# more than 1 sample
CNA.object <- CNA(genomdat = cbind(coriell$Coriell.05296, coriell$Coriell.13330), chrom = coriell$Chromosome, maploc = coriell$Position, data.type = "logratio", sampleid = c("c05296", "c13330"))
smoothed.CNA.object <- smooth.CNA(CNA.object)
DNAcopy.data <- segment(smoothed.CNA.object, verbose=1)

cnv.call <- loadCopyNumberCallsDNAcopy(DNAcopy.data = DNAcopy.data)

bernatgel/CopyNumberPlots documentation built on Sept. 22, 2023, 1:53 a.m.