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Last data update: 2014.03.03

R: Plot the color bias density plot of Illumina Infinium...

plotColorBias1D

R Documentation

Plot the color bias density plot of Illumina Infinium Methylation data

Description

Plot the color bias density plot of Illumina Infinium Methylation data in one dimension (comparing with 2D scatter plot)

Usage

plotColorBias1D(methyLumiM, channel = c("both", "unmethy", "methy", "sum"), colorMode=TRUE, removeGenderProbes = FALSE, logMode = TRUE, subset = NULL, ...)

Arguments

`methyLumiM`	MethyLumiM-class object or eSet-class object, which include methylated and unmethylated probe intensities
`channel`	estimate the intensity in different methods
`colorMode`	whether separate two color channels or not
`removeGenderProbes`	determine whether exclude probes on X and Y chromosomes if the chromosome information is provided in the methyLumiM object.
`logMode`	Whether plot the intensities in log-scale
`subset`	plot subset of randomly selected rows. All data will be plotted if it is NULL.
`...`	other parameters used by `density` and `plot`

Details

Plot the color bias density plot of Illumina Infinium Methylation data. There are four options using "channel" parameter to plot the density plot. "both": estimate the density by pooling together methylated and unmethylated probe intensities. "unmethy" and "methy": plot either unmethylated or methylated probe density. "sum" plot the density of the sum of methylatled and unmethylated probe intensitys.

Value

Invisibly return TRUE if plot successfully.

Author(s)

Pan DU

Examples

data(example.lumiMethy)
# before adjustment
plotColorBias1D(example.lumiMethy)

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(lumi)
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")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumi/plotColorBias1D.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotColorBias1D
> ### Title: Plot the color bias density plot of Illumina Infinium
> ###   Methylation data
> ### Aliases: plotColorBias1D
> ### Keywords: methods hplot
> 
> ### ** Examples
> 
> data(example.lumiMethy)
> # before adjustment
> plotColorBias1D(example.lumiMethy)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>