Function for binning a genome.

Description

Function for generating a GRanges representation of a binning of the genome given in the reference object.

Usage

binGenome(reference, binsize = 1e+06, chroms = seqnames(reference))

Arguments

Details

This function creates a GRanges object that represents bins of size binsize along the genome represented by the reference object.

Value

A GRanges object that represents bins of size binsize along the genome represented by the reference object, includes special handling of chromosomes shorter than binsize and the last bin of each chromosome.

Author(s)

Paul Theodor Pyl

See Also

defineBlocks

Examples

library(BSgenome.Hsapiens.NCBI.GRCh38)
bins <- binGenome(Hsapiens, binsize = 100e6, chroms = c("1","2","3","X","MT"))
bins

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(h5vc)
Loading required package: grid
Loading required package: gridExtra
Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/h5vc/binGenome.Rd_%03d_medium.png", width=480, height=480)
> ### Name: binGenome
> ### Title: Function for binning a genome.
> ### Aliases: binGenome
> 
> ### ** Examples
> 
> library(BSgenome.Hsapiens.NCBI.GRCh38)
Loading required package: BSgenome
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 object is masked from 'package:gridExtra':

    combine

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: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> bins <- binGenome(Hsapiens, binsize = 100e6, chroms = c("1","2","3","X","MT"))
> bins
GRanges object with 11 ranges and 0 metadata columns:
       seqnames                 ranges strand
          <Rle>              <IRanges>  <Rle>
   [1]        1 [        1, 100000000]      *
   [2]        1 [100000001, 200000000]      *
   [3]        1 [200000001, 248956422]      *
   [4]        2 [        1, 100000000]      *
   [5]        2 [100000001, 200000000]      *
   [6]        2 [200000001, 242193529]      *
   [7]        3 [        1, 100000000]      *
   [8]        3 [100000001, 198295559]      *
   [9]        X [        1, 100000000]      *
  [10]        X [100000001, 156040895]      *
  [11]       MT [        1,     16569]      *
  -------
  seqinfo: 5 sequences from an unspecified genome
> 
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> dev.off()
null device 
          1 
>