plot cut frequencies of RE sites along a given chromosome

Description

plot cut frequencies of RE sites along a chromosome, which gives a bird-eye view of genome-wide frequent-cut regions and RE inaccessible regions.

Usage

plotCutDistribution(assignedSeqs,REmap, chr="chr1",xlim, 
title="RE cut frequency distribution",
xlab="Chromosome Location (bp)",ylab="Frequency", 
round=TRUE, n.sequence)

Arguments

Author(s)

Lihua Julie Zhu

See Also

assignSeq2REsite, distanceHistSeq2RE

Examples

	library(REDseq)
	data(example.assignedREDseq)
	data(example.map)
	plotCutDistribution(example.assignedREDseq,example.map,
chr="2", xlim =c(3012000, 3020000))

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(REDseq)
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: BSgenome.Celegans.UCSC.ce2
Loading required package: BSgenome
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
Loading required package: multtest
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ChIPpeakAnno
Loading required package: grid
Loading required package: VennDiagram
Loading required package: futile.logger

No methods found in "IRanges" for requests: %in%
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/REDseq/plotCutDistribution.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotCutDistribution
> ### Title: plot cut frequencies of RE sites along a given chromosome
> ### Aliases: plotCutDistribution
> ### Keywords: graph
> 
> ### ** Examples
> 
> 	library(REDseq)
> 	data(example.assignedREDseq)
> 	data(example.map)
> 	plotCutDistribution(example.assignedREDseq,example.map,
+ chr="2", xlim =c(3012000, 3020000))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>