Estimate intensity of Illumina methylation data

Description

Estimate intensity of Illumina methylation data, which is the sum of Illumina methylated and unmethylated probe intensities

Usage

estimateIntensity(methyLumiM, returnType=c("ExpressionSet", "matrix"))

Arguments

Details

The Intensity basically is the sum of Illumina methylated and unmethylated probe intensities.

Value

An ExpressionSet or matrix object of methylation Intensity-value

Author(s)

Pan DU

See Also

See Also as estimateBeta and estimateM

Examples

data(example.lumiMethy)
methyLumiIntensity = estimateIntensity(example.lumiMethy)
boxplot(methyLumiIntensity)

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 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> 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/estimateIntensity.Rd_%03d_medium.png", width=480, height=480)
> ### Name: estimateIntensity
> ### Title: Estimate intensity of Illumina methylation data
> ### Aliases: estimateIntensity
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(example.lumiMethy)
> methyLumiIntensity = estimateIntensity(example.lumiMethy)
> boxplot(methyLumiIntensity)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>