Extract genomic ranges for a given bin

Description

For genomic ranges with N bins, extract the Genomic ranges for a given bin.

Usage

extractBinGRanges(GenoRanges, bin, nbins)

Arguments

Value

A GRanges Object

Author(s)

Mattia Pelizzola

See Also

mapBSdata2GRangesBin

Examples

gr_file <- system.file('extdata', 'GR_chr20.Rdata', package='methylPipe')
load(gr_file)
extractBinGRanges(GR_chr20, 2, 5)

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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> library(methylPipe)
Loading required package: 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
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/methylPipe/extractBinGRanges.Rd_%03d_medium.png", width=480, height=480)
> ### Name: extractBinGRanges
> ### Title: Extract genomic ranges for a given bin
> ### Aliases: extractBinGRanges
> 
> ### ** Examples
> 
> gr_file <- system.file('extdata', 'GR_chr20.Rdata', package='methylPipe')
> load(gr_file)
> extractBinGRanges(GR_chr20, 2, 5)
GRanges object with 14 ranges and 0 metadata columns:
       seqnames           ranges strand
          <Rle>        <IRanges>  <Rle>
   [1]    chr20 [ 15150,  15949]      *
   [2]    chr20 [ 70051,  70850]      *
   [3]    chr20 [ 84985,  85784]      *
   [4]    chr20 [117064, 117863]      *
   [5]    chr20 [154724, 155523]      *
   ...      ...              ...    ...
  [10]    chr20 [274169, 274968]      *
  [11]    chr20 [308107, 308906]      *
  [12]    chr20 [335508, 336307]      *
  [13]    chr20 [389987, 390786]      *
  [14]    chr20 [471282, 472081]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>