Color bias adjust of Illumina Infinium methylation data

Description

Color bias adjust of Illumina Infinium methylation data, which is an object in MethyLumiM class.

Usage

lumiMethyC(methyLumiM, method = c("quantile", "ssn", "none"), verbose = TRUE, overwriteBigMatrix=FALSE, ...)

Arguments

Details

The first two arguments of the user defined function should be two intensity matrix (pool of methylated and unmethylated probe intensities) of red and green channel respectively. The return of the user defined function should be a list including color adjusted matrix of red and green channel. For example: return(list(red=redData, green=grnData)). "redData" and "grnData" are two color adjusted matrix.

Value

Return an object (same class as input methyLumiM) with updated "methylated" and "unmethylated" data matrix after background level adjustment.

Author(s)

Pan DU

See Also

See Also adjColorBias.quantile and adjColorBias.ssn

Examples

data(example.lumiMethy)
# before adjustment
plotColorBias1D(example.lumiMethy)
# plot in 2D plot of one selected sample
plotColorBias2D(example.lumiMethy, selSample = 1)
lumiMethy.adj = lumiMethyC(example.lumiMethy)
# after adjustment
plotColorBias1D(lumiMethy.adj)
# plot in 2D plot of one selected sample
plotColorBias2D(lumiMethy.adj, selSample = 1)

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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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/lumiMethyC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiMethyC
> ### Title: Color bias adjust of Illumina Infinium methylation data
> ### Aliases: lumiMethyC
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(example.lumiMethy)
> # before adjustment
> plotColorBias1D(example.lumiMethy)
> # plot in 2D plot of one selected sample
> plotColorBias2D(example.lumiMethy, selSample = 1)
> lumiMethy.adj = lumiMethyC(example.lumiMethy)
Perform quantile color balance adjustment ...
Processing sample Treat1 ...
Processing sample Treat2 ...
Processing sample Treat3 ...
Processing sample Treat4 ...
Processing sample Ctrl1 ...
Processing sample Ctrl2 ...
Processing sample Ctrl3 ...
Processing sample Ctrl4 ...
Processing sample Treat1.rep ...
Processing sample Treat2.rep ...
Processing sample Treat3.rep ...
Processing sample Treat4.rep ...
Processing sample Ctrl1.rep ...
Processing sample Ctrl2.rep ...
Processing sample Ctrl3.rep ...
Processing sample Ctrl4.rep ...
> # after adjustment
> plotColorBias1D(lumiMethy.adj)
> # plot in 2D plot of one selected sample
> plotColorBias2D(lumiMethy.adj, selSample = 1)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>