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

Description Usage Arguments Value Author(s) Examples

Description

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

Usage

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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

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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))

HPCBio/MEDIPS-BioC documentation built on May 30, 2019, 12:44 p.m.