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Last data update: 2014.03.03

R: Plot the beta value distributions of the Infinium I and II...

densityByProbeType

R Documentation

Plot the beta value distributions of the Infinium I and II probe types relative to the overall beta value distribution.

Description

Plot the overall density distribution of beta values and the density distributions of the Infinium I and II probe types.

Usage

densityByProbeType(data, legendPos = "top", colors = c("black", "red", "blue"), main = "", lwd = 3, cex.legend = 1)

Arguments

`data`	A `MethylSet` or a `matrix` or a `vector`. We either use the `getBeta` function to get Beta values (in the first case) or we assume the matrix or vector contains Beta values.
`legendPos`	The x and y co-ordinates to be used to position the legend. They can be specified by keyword or in any way which is accepted by `xy.coords`. See `legend` for details.
`colors`	Colors to be used for the different beta value density distributions. Must be a vector of length 3.
`main`	Plot title.
`lwd`	The line width to be used for the different beta value density distributions.
`cex.legend`	The character expansion factor for the legend text.

Details

The density distribution of the beta values for a single sample is plotted. The density distributions of the Infinium I and II probes are then plotted individually, showing how they contribute to the overall distribution. This is useful for visualising how using SWAN affects the data.

Author(s)

Jovana Maksimovic jovana.maksimovic@mcri.edu.au.

References

No return value. Plot is produced as a side-effect.

Examples

if (require(minfi) & require(minfiData)) {
  dat <- preprocessRaw(RGsetEx)
  datSwan <- SWAN(dat)
  par(mfrow=c(1,2))
  densityByProbeType(dat[,1], main="Raw")
  densityByProbeType(datSwan[,1], main="SWAN")
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(missMethyl)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/missMethyl/densityByProbeType.Rd_%03d_medium.png", width=480, height=480)
> ### Name: densityByProbeType
> ### Title: Plot the beta value distributions of the Infinium I and II probe
> ###   types relative to the overall beta value distribution.
> ### Aliases: densityByProbeType
> 
> ### ** Examples
> 
> if (require(minfi) & require(minfiData)) {
+   dat <- preprocessRaw(RGsetEx)
+   datSwan <- SWAN(dat)
+   par(mfrow=c(1,2))
+   densityByProbeType(dat[,1], main="Raw")
+   densityByProbeType(datSwan[,1], main="SWAN")
+ }
Loading required package: minfi
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: 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: 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: minfiData
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
[SWAN] Preparing normalization subset
[SWAN] Normalizing methylated channel
[SWAN] Normalizing unmethylated channel
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>