Extend Regions

Description

Extends the regions a number of bases at each end. Negative numbers will reduce the region instead of enlarging it.

Usage

extendRegions(A, extend.start=0, extend.end=0)

Arguments

Value

a GenomicRanges object with the extended regions.

Note

If negative values are provided and the new extremes are "flipped", the function will fail. It does not check if the extended regions fit into the genome.

See Also

plotRegions, toDataframe, toGRanges, subtractRegions, splitRegions, overlapRegions, commonRegions, mergeRegions, joinRegions

Examples

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

extend1 <- extendRegions(A, extend.start=5, extend.end=2)

extend2 <- extendRegions(A, extend.start=15)

extend3 <- extendRegions(A, extend.start=-1)

plotRegions(list(A, extend1, extend2, extend3), chromosome="chr1", regions.labels=c("A", "extend1", "extend2", "extend3"), regions.colors=4:1)

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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Type 'demo()' for some demos, 'help()' for on-line help, or
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> 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/extendRegions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: extendRegions
> ### Title: Extend Regions
> ### Aliases: extendRegions
> 
> ### ** Examples
> 
> A <- data.frame("chr1", c(10, 20, 30), c(13, 28, 40))
> 
> extend1 <- extendRegions(A, extend.start=5, extend.end=2)
> 
> extend2 <- extendRegions(A, extend.start=15)
> 
> extend3 <- extendRegions(A, extend.start=-1)
> 
> plotRegions(list(A, extend1, extend2, extend3), chromosome="chr1", regions.labels=c("A", "extend1", "extend2", "extend3"), regions.colors=4:1)
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>