Transform GRangesList to GRanges

Description

Transform GRangesList to GRanges.

Usage

flatGrl(object, indName = "grl_name")

Arguments

Details

This method is different from default stack, it integrate elementMetadata of GRangesList to the final coerced GRanges.

Value

A GRanges object.

Author(s)

Tengfei Yin

Examples

library(GenomicRanges)
gr1 <- GRanges("chr1", IRanges(1:10, width = 5))
gr2 <- GRanges("chr2", IRanges(1:10, width = 5))
obj <- GRangesList(gr1, gr2)
values(obj) <- data.frame(a = 1:2, b = letters[1:2])
stack(obj)
flatGrl(obj)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(biovizBase)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/biovizBase/flatGrl.Rd_%03d_medium.png", width=480, height=480)
> ### Name: flatGrl
> ### Title: Transform GRangesList to GRanges
> ### Aliases: flatGrl
> 
> ### ** Examples
> 
> library(GenomicRanges)
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> gr1 <- GRanges("chr1", IRanges(1:10, width = 5))
> gr2 <- GRanges("chr2", IRanges(1:10, width = 5))
> obj <- GRangesList(gr1, gr2)
> values(obj) <- data.frame(a = 1:2, b = letters[1:2])
> stack(obj)
GRanges object with 20 ranges and 1 metadata column:
       seqnames    ranges strand | sample
          <Rle> <IRanges>  <Rle> |  <Rle>
   [1]     chr1    [1, 5]      * |      1
   [2]     chr1    [2, 6]      * |      1
   [3]     chr1    [3, 7]      * |      1
   [4]     chr1    [4, 8]      * |      1
   [5]     chr1    [5, 9]      * |      1
   ...      ...       ...    ... .    ...
  [16]     chr2  [ 6, 10]      * |      2
  [17]     chr2  [ 7, 11]      * |      2
  [18]     chr2  [ 8, 12]      * |      2
  [19]     chr2  [ 9, 13]      * |      2
  [20]     chr2  [10, 14]      * |      2
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
> flatGrl(obj)
GRanges object with 20 ranges and 3 metadata columns:
       seqnames    ranges strand | grl_name         a        b
          <Rle> <IRanges>  <Rle> |    <Rle> <integer> <factor>
   [1]     chr1    [1, 5]      * |        1         1        a
   [2]     chr1    [2, 6]      * |        1         1        a
   [3]     chr1    [3, 7]      * |        1         1        a
   [4]     chr1    [4, 8]      * |        1         1        a
   [5]     chr1    [5, 9]      * |        1         1        a
   ...      ...       ...    ... .      ...       ...      ...
  [16]     chr2  [ 6, 10]      * |        2         2        b
  [17]     chr2  [ 7, 11]      * |        2         2        b
  [18]     chr2  [ 8, 12]      * |        2         2        b
  [19]     chr2  [ 9, 13]      * |        2         2        b
  [20]     chr2  [10, 14]      * |        2         2        b
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>