R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Circular Randomize Regions

circularRandomizeRegions

R Documentation

Circular Randomize Regions

Description

Given a set of regions A and a genome, this function returns a new set of regions created by applying a random spin to each chromosome.

Usage

circularRandomizeRegions(A, genome="hg19", mask=NULL, max.mask.overlap=NULL, max.retries=10, verbose=TRUE, ...)

Arguments

`A`	The set of regions to randomize. A region set in any of the accepted formats by `toGRanges` (`GenomicRanges`, `data.frame`, etc...)
`genome`	The reference genome to use. A valid genome object. Either a `GenomicRanges` or `data.frame` containing one region per whole chromosome or a character uniquely identifying a genome in `BSgenome` (e.g. "hg19", "mm10" but not "hg"). Internally it uses `getGenomeAndMask`.
`mask`	The set of regions specifying where a random region can not be (centromeres, repetitive regions, unmappable regions...). A region set in any of the accepted formats by `toGRanges` (`GenomicRanges`,`data.frame`, ...). If `NULL` it will try to derive a mask from the genome (currently only works is the genome is a character string) and if `NA` it will explicitly give an empty mask.
`max.mask.overlap`	numeric value
`max.retries`	numeric value
`verbose`	a boolean.
`...`	further arguments to be passed to or from methods.

Details

This randomization strategy is useful when the spatial relation between the regions in the RS is important and has to be conserved.

Value

It returns a GenomicRanges object with the regions resulting from the randomization process.

Examples

A <- data.frame("chr1", c(1, 10, 20, 30), c(12, 13, 28, 40))

mask <- data.frame("chr1", c(20000000, 100000000), c(22000000, 130000000))

genome <- data.frame(c("chr1", "chr2"), c(1, 1), c(180000000, 20000000))

circularRandomizeRegions(A)

circularRandomizeRegions(A, genome=genome, mask=mask, per.chromosome=TRUE, non.overlapping=TRUE)

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(regioneR)
Loading required package: memoise
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: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/regioneR/circularRandomizeRegions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: circularRandomizeRegions
> ### Title: Circular Randomize Regions
> ### Aliases: circularRandomizeRegions
> 
> ### ** Examples
> 
> A <- data.frame("chr1", c(1, 10, 20, 30), c(12, 13, 28, 40))
> 
> mask <- data.frame("chr1", c(20000000, 100000000), c(22000000, 130000000))
> 
> genome <- data.frame(c("chr1", "chr2"), c(1, 1), c(180000000, 20000000))
> 
> circularRandomizeRegions(A)
GRanges object with 4 ranges and 0 metadata columns:
      seqnames               ranges strand
         <Rle>            <IRanges>  <Rle>
  [1]     chr1 [83203907, 83203918]      *
  [2]     chr1 [83203916, 83203919]      *
  [3]     chr1 [83203926, 83203934]      *
  [4]     chr1 [83203936, 83203946]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> circularRandomizeRegions(A, genome=genome, mask=mask, per.chromosome=TRUE, non.overlapping=TRUE)
GRanges object with 4 ranges and 0 metadata columns:
      seqnames               ranges strand
         <Rle>            <IRanges>  <Rle>
  [1]     chr1 [83057189, 83057200]      *
  [2]     chr1 [83057198, 83057201]      *
  [3]     chr1 [83057208, 83057216]      *
  [4]     chr1 [83057218, 83057228]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>