getGRangesFormat: Get segments on the GRanges format

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

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.

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.

Value

The segments converted to the GRanges container class.

Author(s)

Gro Nilsen

Examples

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

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