Retrieve a subset of segments
This function returns a subset of segments according to the input and the specified chromosomes and/or samples.
subsetSegments(segments, chrom = NULL, sample = NULL, sep="\t", ...)
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 |
chrom |
a numeric or character vector with chromosome(s) for which segments should be selected. If unspecified, all chromosomes in |
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 |
sep |
the separator of the input files if |
... |
optional parameters to be passed to |
A data frame containing the desired subset of segments.
Gro Nilsen
#Load lymphoma data data(lymphoma) #Select segments only for samples 1 and 6 and chromosomes 1:9: segments <- pcf(lymphoma,gamma=12) sub.segments <- subsetSegments(segments=segments,chrom=c(1:9),sample=c(1,6))
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