Plot of the region

Description

Plot of the beta values againts their position. Data is taken from probe analysis. Cpgs with a p-value smaller than 0.05 (without adjusting) are blue and points with a p-value greater than 0.05 are red.

Usage

plotRegion(object, variable = modelVariables(object)[[1]], range = NULL)

Arguments

Value

A plot is generated on the current graphics device.

Examples

if (require(minfiData) & require(GenomicRanges)){
set <- prepareMethylationSet(getBeta(MsetEx), pheno = pData(MsetEx))
range <- GenomicRanges::GRanges(seqnames=Rle("chrY"), 
ranges = IRanges(3000000, end=12300000))
rangeNoSNPs <- DARegionAnalysis(set, variable_names = "sex", range = range)
plotRegion(rangeNoSNPs)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/plotRegion-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotRegion
> ### Title: Plot of the region
> ### Aliases: plotRegion
> 
> ### ** Examples
> 
> if (require(minfiData) & require(GenomicRanges)){
+ set <- prepareMethylationSet(getBeta(MsetEx), pheno = pData(MsetEx))
+ range <- GenomicRanges::GRanges(seqnames=Rle("chrY"), 
+ ranges = IRanges(3000000, end=12300000))
+ rangeNoSNPs <- DARegionAnalysis(set, variable_names = "sex", range = range)
+ plotRegion(rangeNoSNPs)
+ }
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
Loading required package: rngtools
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:S4Vectors':

    new2

The following object is masked from 'package:base':

    isNamespaceLoaded

Your contrast returned 123 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Fitting chrY...
Demarcating regions...
Done!
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>