CNA: Create 'Copy Number Array' data object

In veseshan/DNAcopy: DNA Copy Number Data Analysis

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, presorted = FALSE)
  ## S3 method for class 'CNA'
print(x, ...)

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.
presorted	logical indicator telling if the data have already been sorted by chrom and maploc. Default is FALSE.
x	object returned by CNA
...	arguments to be passed onto print command called within.

Details

Data that are NA, Inf, NaN will be removed on a per sample basis for "genomdat" and all samples for "chrom" and "maploc".

If the chrom variable has non-numeric values make it into an ordered variable to get them ordered correctly. E.g. for human genome use: chrom <- ordered(chrom, levels=c(1:22,"X","Y")) to prepare the variable if chromosomes X and Y are present in your data.

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"))

veseshan/DNAcopy documentation built on Oct. 18, 2023, 8:30 p.m.