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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(copynumber)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/copynumber/getGRangesFormat.rd_%03d_medium.png", width=480, height=480)
> ### Name: getGRangesFormat
> ### Title: Get segments on the GRanges format
> ### Aliases: getGRangesFormat
> 
> ### ** Examples
> 
> #load lymphoma data
> data(lymphoma)
> #Run pcf
> seg <- pcf(data=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 
> #Obtain the GRanges format
> gr <- getGRangesFormat(seg)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>