Join Regions

Description

Joins the regions from a region set A that are less than min.dist bases apart.

Usage

joinRegions(A, min.dist=1)

Arguments

Value

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

Note

All metadata (additional columns in the region set in addition to chromosome, start and end) will be ignored and not present in the returned region set.

The implementation relies completely in the reduce function from IRanges package.

See Also

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

Examples

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

join1 <- joinRegions(A)

join2 <- joinRegions(A, min.dist=3)

join3 <- joinRegions(A, min.dist=10)

plotRegions(list(A, join1, join2, join3), chromosome="chr1", regions.labels=c("A", "join1", "join2", "join3"), 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/joinRegions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: joinRegions
> ### Title: Join Regions
> ### Aliases: joinRegions
> 
> ### ** Examples
> 
> A <- data.frame("chr1", c(1, 10, 20, 30), c(12, 13, 28, 40))
> 
> join1 <- joinRegions(A)
> 
> join2 <- joinRegions(A, min.dist=3)
> 
> join3 <- joinRegions(A, min.dist=10)
> 
> plotRegions(list(A, join1, join2, join3), chromosome="chr1", regions.labels=c("A", "join1", "join2", "join3"), regions.colors=4:1)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>