Artificial Human Chromosome for Testing Purposes

Description

A GRanges object defining a minimalistic artificial human chromosome with 200,000 bp length

Usage

hgA

Format

Real human genome-based examples would require the supply of massive data and would require lengthy computation times. Therefore, the examples supplied with this package are based on a small single-chromosome artificial genome. The GRanges object hgA provides a description of this artificial genome that can be used for further processing, e.g. by the partitionRegions function.

Author(s)

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

References

http://www.bioinf.jku.at/software/podkat

See Also

GRanges, partitionRegions

Examples

## load data set
data(hgA)

## display hgA
show(hgA)
genome(hgA)

## partition hgA into overlapping regions of length 10,000 bp
partitionRegions(hgA, width=10000)

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(podkat)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/podkat/hgA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hgA
> ### Title: Artificial Human Chromosome for Testing Purposes
> ### Aliases: hgA
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## load data set
> data(hgA)
> 
> ## display hgA
> show(hgA)
GRanges object with 1 range and 0 metadata columns:
      seqnames      ranges strand
         <Rle>   <IRanges>  <Rle>
  [1]     chr1 [1, 200000]      *
  -------
  seqinfo: 1 sequence from hgA genome
> genome(hgA)
 chr1 
"hgA" 
> 
> ## partition hgA into overlapping regions of length 10,000 bp
> partitionRegions(hgA, width=10000)
GRanges object with 39 ranges and 0 metadata columns:
       seqnames           ranges strand
          <Rle>        <IRanges>  <Rle>
   [1]     chr1   [    1, 10000]      *
   [2]     chr1   [ 5001, 15000]      *
   [3]     chr1   [10001, 20000]      *
   [4]     chr1   [15001, 25000]      *
   [5]     chr1   [20001, 30000]      *
   ...      ...              ...    ...
  [35]     chr1 [170001, 180000]      *
  [36]     chr1 [175001, 185000]      *
  [37]     chr1 [180001, 190000]      *
  [38]     chr1 [185001, 195000]      *
  [39]     chr1 [190001, 200000]      *
  -------
  seqinfo: 1 sequence from hgA genome
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>