Estimate methylation Beta-value matrix

Description

Estimate methylation Beta-value matrix from MethyLumiM-class object or eSet-class object, which include methylated and unmethylated probe intensities

Usage

estimateBeta(methyLumiM, returnType=c("ExpressionSet", "matrix"), offset = 100)

Arguments

Details

Beta-value is ratio between Illumina methylated probe intensity and total probe intensities (sum of methylated and unmethylated probe intensities, see estimateIntensity). An offset value added to the denominator to avoid close to zero intensities in the denominator. Beta-value is in the range of 0 and 1. If we assume the probe intensity follows Gamma distribution, then the Beta-value follows a Beta distribution.

Value

An ExpressionSet or matrix object of methylation Beta-value

Author(s)

Pan DU

See Also

See Also as estimateIntensity and estimateM

Examples

data(example.lumiMethy)
methyLumiBeta = estimateBeta(example.lumiMethy)
density(methyLumiBeta)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/estimateBeta.Rd_%03d_medium.png", width=480, height=480)
> ### Name: estimateBeta
> ### Title: Estimate methylation Beta-value matrix
> ### Aliases: estimateBeta
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(example.lumiMethy)
> methyLumiBeta = estimateBeta(example.lumiMethy)
> density(methyLumiBeta)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>