subsetData {copynumber} | R Documentation

## Retrieve a data subset

### Description

This function returns a subset of copy number data according to the input and the specified chromosomes and/or samples.

### Usage

     subsetData(data, chrom = NULL, sample = NULL, sep="\t", ...)

### Arguments

`data` | either a data frame or the name of a tab-separated file from which copy number data can be read. The rows of the data frame or file should represent the probes. Column 1 must hold numeric or character chromosome numbers, column 2 the numeric local probe positions, and subsequent columns the numeric copy number measurements for one or more samples.
`chrom` | a numeric or character vector with chromosome(s) for which data should be selected. If unspecified, all chromosomes in `data` will be selected.
`sample` | a numeric vector indicating for which sample(s) data should be selected. The number(s) should correspond to the sample's place (in order of appearance) in `data`.
`sep` | the separator of the input files if `data`. Default is tab.
`...` | optional parameters to be passed to `read.table` in the case where `data` is to be read from file.

### Value

A data frame containing the desired subset of data.

### Author(s)

Gro Nilsen

### Examples

    #Load lymphoma data
    data(lymphoma)

    #Select data only for samples 1 and 6 and chromosomes 1:9:
    sub.data <- subsetData(data=lymphoma,chrom=c(1:9),sample=c(1,6))

[Package copynumber version 1.24.0 Index]