Retrieve a subset of segments

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

Usage

subsetSegments(segments, chrom = NULL, sample = NULL, sep = "\t", ...)

Arguments

segments

either a data frame or the name of a tab-separated file from which segmentation results can be read. Segmentation results may come from pcf(), multipcf() or aspcf().

chrom

a numeric or character vector with chromosome(s) for which segments should be selected. If unspecified, all chromosomes in segments will be selected.

sample

a numeric vector indicating for which sample(s) segments should be selected. The number(s) should correspond to the sample's place (in order of appearance) in segments.

sep

the separator of the input files if segments is a file. Default is tab.

...

optional parameters to be passed to read.table in the case where segments is to be read from file.

Value

A data frame containing the desired subset of segments.

Author

Gro Nilsen

Examples

#Load lymphoma data
data(lymphoma)

#Select segments only for samples 1 and 6 and chromosomes 1:9:
segments <- pcf(lymphoma,gamma=12)
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 1q 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 2q 
#> pcf finished for chromosome arm 3p 
#> pcf finished for chromosome arm 3q 
#> pcf finished for chromosome arm 4p 
#> pcf finished for chromosome arm 4q 
#> pcf finished for chromosome arm 5p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6p 
#> pcf finished for chromosome arm 6q 
#> pcf finished for chromosome arm 7p 
#> pcf finished for chromosome arm 7q 
#> pcf finished for chromosome arm 8p 
#> pcf finished for chromosome arm 8q 
#> pcf finished for chromosome arm 9p 
#> pcf finished for chromosome arm 9q 
#> pcf finished for chromosome arm 10p 
#> pcf finished for chromosome arm 10q 
#> pcf finished for chromosome arm 11p 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 12p 
#> pcf finished for chromosome arm 12q 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 14q 
#> pcf finished for chromosome arm 15q 
#> pcf finished for chromosome arm 16p 
#> pcf finished for chromosome arm 16q 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 17q 
#> pcf finished for chromosome arm 18p 
#> pcf finished for chromosome arm 18q 
#> pcf finished for chromosome arm 19p 
#> pcf finished for chromosome arm 19q 
#> pcf finished for chromosome arm 20p 
#> pcf finished for chromosome arm 20q 
#> pcf finished for chromosome arm 21q 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm 23p 
#> pcf finished for chromosome arm 23q 
sub.segments <- subsetSegments(segments=segments,chrom=c(1:9),sample=c(1,6))