Plot the distance distribution from sequence to the associated RE sites

Description

Give an overview of the distance distribution from all assigned sequences to the associated RE sites. If average or estimate is used for assigning sequences to RE sites, the count for histogram drawing will be adjusted with the weight assigned.

Usage

distanceHistSeq2RE(assignedSeqs, longestDist = 1000, 
title = "histogram of distance to assigned RE site", 
xlab = "Distance to assigned RE site", ylab = "Frequency", ylim="")

Arguments

Author(s)

Lihua Julie Zhu

See Also

assignSeq2REsite, distanceHistSeq2RE

Examples

library(REDseq)
data(example.assignedREDseq)
distanceHistSeq2RE(example.assignedREDseq,ylim=c(0,20))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/distanceHistSeq2RE.Rd_%03d_medium.png", width=480, height=480)
> ### Name: distanceHistSeq2RE
> ### Title: Plot the distance distribution from sequence to the associated
> ###   RE sites
> ### Aliases: distanceHistSeq2RE
> ### Keywords: graph
> 
> ### ** Examples
> 
> library(REDseq)
> data(example.assignedREDseq)
> distanceHistSeq2RE(example.assignedREDseq,ylim=c(0,20))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>