copynumber (version 1.12.0)

getGRangesFormat: Get segments on the GRanges format

Description

The segments data frame obtained e.g. by pcf, multipcf or aspcf is converted to the GRanges format.

Usage

getGRangesFormat(segments)

Arguments

segments

a data frame containing segmentation results found by e.g. pcf, multipcf or aspcf.

Value

• The segments converted to the GRanges container class.

Details

GRanges, in the GenomicRanges package, is the standard BioConductor containers for range data. For some applications it may therefore be useful to convert segmentation results to this format.

Examples

#load lymphoma data
data(lymphoma)
#Run pcf
seg <- pcf(data=lymphoma,gamma=12)
#Obtain the GRanges format
gr <- getGRangesFormat(seg)