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Last data update: 2014.03.03

R: Function plots the results of the MEDIPS.seqCoverage...

MEDIPS.plotSeqCoverage

R Documentation

Function plots the results of the MEDIPS.seqCoverage function.

Description

The results of the sequence pattern coverage analysis will be visualized in two possible ways.

Usage

MEDIPS.plotSeqCoverage(seqCoverageObj=NULL, main=NULL, type="pie", cov.level = c(0,1,2,3,4,5), t="Inf")

Arguments

`seqCoverageObj`	The coverage results object returned by the MEDIPS.seqCoverage function.
`main`	The title of the coverage plot.
`type`	there are two types of visualization. The pie chart (default) illustrates the fraction of CpGs covered by the given reads at different coverage level (see also the parameter cov.level). As an alternative, a histogram over all coverage level can be ploted ("hist").
`cov.level`	The pie chart illustrates the fraction of CpGs covered by the given reads according to their coverage level. The visualized coverage levels can be adjusted by the cov.level parameter.
`t`	specifies the maximal coverage depth to be plotted, if type="hist"

Value

The sequence pattern coverage plot will be visualized.

Author(s)

Lukas Chavez

Examples


library(MEDIPSData)
library(BSgenome.Hsapiens.UCSC.hg19)
bam.file.hESCs.Rep1.MeDIP = system.file("extdata", "hESCs.MeDIP.Rep1.chr22.bam", package="MEDIPSData")

cr=MEDIPS.seqCoverage(file=bam.file.hESCs.Rep1.MeDIP, pattern="CG", BSgenome="BSgenome.Hsapiens.UCSC.hg19", chr.select="chr22", extend=250, shift=0, uniq=1e-3, paired=FALSE)

MEDIPS.plotSeqCoverage(seqCoverageObj=cr, main="Sequence pattern coverage", type="pie", cov.level = c(0,1,2,3,4,5))

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(MEDIPS)
Loading required package: BSgenome
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: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MEDIPS/MEDIPS.plotSeqCoverage.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MEDIPS.plotSeqCoverage
> ### Title: Function plots the results of the MEDIPS.seqCoverage function.
> ### Aliases: MEDIPS.plotSeqCoverage
> 
> ### ** Examples
> 
> 
> library(MEDIPSData)
> library(BSgenome.Hsapiens.UCSC.hg19)
> bam.file.hESCs.Rep1.MeDIP = system.file("extdata", "hESCs.MeDIP.Rep1.chr22.bam", package="MEDIPSData")
> 
> cr=MEDIPS.seqCoverage(file=bam.file.hESCs.Rep1.MeDIP, pattern="CG", BSgenome="BSgenome.Hsapiens.UCSC.hg19", chr.select="chr22", extend=250, shift=0, uniq=1e-3, paired=FALSE)
Reading bam alignment hESCs.MeDIP.Rep1.chr22.bam 
Selecting  chr22 
Total number of imported short reads: 152586
Extending reads...
Creating GRange Object...
Keep at most 1 read(s) mapping to the same genomic location
Number of remaining reads: 150793
Loading chromosome lengths for BSgenome.Hsapiens.UCSC.hg19...
Get genomic sequence pattern positions...
Searching in chr22 ...[ 578097 ] found.
Number of identified  CG  pattern:  578097 
Calculating sequence pattern coverage...
> 
> MEDIPS.plotSeqCoverage(seqCoverageObj=cr, main="Sequence pattern coverage", type="pie", cov.level = c(0,1,2,3,4,5))
Creating summary...
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>