subsetData: Retrieve a data subset

In igordot/copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

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))

igordot/copynumber documentation built on Sept. 18, 2020, 8:48 a.m.