Last data update: 2014.03.03

R: Make a Volcano plot with the probe results
plotVolcanoR Documentation

Make a Volcano plot with the probe results

Description

Plot log p-value versus the change in expression/methylation.

Usage

plotVolcano(object, variable = modelVariables(object)[1], mindiff = NULL)

Arguments

object

MethylationResults or MethylationRegionResults

variable

Character with the variable name used to obtain the probe results. Note: model name should be used. Original variable name might not be valid.

mindiff

Numeric with the minimum change in methylation or expression needed to be significant

Value

A plot is generated on the current graphics device.

Examples

if (require(minfiData)){
betas <- getBeta(MsetEx)[floor(seq(1, nrow(MsetEx), 10000)), ]
set <- prepareMethylationSet(betas, pheno = pData(MsetEx))
methyOneVar <- DAPipeline(set, variable_names = "sex", probe_method = "ls")
plotEWAS(methyOneVar)
}

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
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MEAL)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: MultiDataSet
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MEAL/plotVolcano-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotVolcano
> ### Title: Make a Volcano plot with the probe results
> ### Aliases: plotVolcano
> 
> ### ** Examples
> 
> if (require(minfiData)){
+ betas <- getBeta(MsetEx)[floor(seq(1, nrow(MsetEx), 10000)), ]
+ set <- prepareMethylationSet(betas, pheno = pData(MsetEx))
+ methyOneVar <- DAPipeline(set, variable_names = "sex", probe_method = "ls")
+ plotEWAS(methyOneVar)
+ }
Loading required package: minfiData
Loading required package: minfi
Loading required package: lattice
Loading required package: GenomicRanges
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: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Your contrast returned 1 individually significant probes; a small but real effect. Consider manually setting the value of pcutoff to return more DMRs, but be warned that doing this increases the risk of Type I errors.
Fitting chr1...
Fitting chr10...
Fitting chr11...
Fitting chr12...
Fitting chr13...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>