CNA {DNAcopy}R Documentation

Create 'Copy Number Array' data object

Description

Creates a `copy number array' data object used for DNA copy number analyses by programs such as circular binary segmentation (CBS).

Usage

  CNA(genomdat, chrom, maploc, data.type=c("logratio","binary"),
                 sampleid=NULL)

Arguments

genomdat a vector or matrix of data from array-CGH, ROMA, or other copy number experiments. If it is a matrix the rows correspond to the markers and the columns to the samples.
chrom the chromosomes (or other group identifier) from which the markers came. Vector of length same as the number of rows of genomdat. If one wants the chromosomes to be ordered in the natural order, this variable should be numeric or ordered category.
maploc the locations of marker on the genome. Vector of length same as the number of rows of genomdat. This has to be numeric.
data.type logratio (aCGH, ROMA, etc.) or binary (LOH).
sampleid sample identifier. If missing the samples are named by prefixing "Sample" to consecutive integers.

Value

An object of class CNA. There is a print method that gives the number of samples and probes and the type of data.

Examples


data(coriell)

#Combine into one CNA object to prepare for analysis on Chromosomes 1-23

CNA.object <- CNA(cbind(coriell$Coriell.05296,coriell$Coriell.13330),
                  coriell$Chromosome,coriell$Position,
                  data.type="logratio",sampleid=c("c05296","c13330"))


[Package DNAcopy version 1.1.0 Index]