Extract intensity data for 613 Illumina negative controls found on 450k arrays.

Description

Extracts the intensity data for the 613 Illumina negative controls found on 450k arrays and returns a matrix of M-values (log2 ratio of the green to red intensities).

Usage

getINCs(rgSet)

Arguments

Details

The getINCs function extracts the intensity data for the INCs from an RGChannelSet object. The function retrieves both the green and red channel intensity values and returns the data as the log2 ratio of the green to red intensities. Essentially, the INCs are being treated like 450k Type II probes for which the M-values are also given as the log2 ratio of the green to red intensities.

Value

An matrix of M-values.

Author(s)

Jovana Maksimovic jovana.maksimovic@mcri.edu.au

See Also

RGChannelSet

Examples

if (require(minfi) & require(minfiData)) {

  INCs <- getINCs(RGsetEx)
  head(INCs)
  dim(INCs)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/getINCs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getINCs
> ### Title: Extract intensity data for 613 Illumina negative controls found
> ###   on 450k arrays.
> ### Aliases: getINCs
> 
> ### ** Examples
> 
> if (require(minfi) & require(minfiData)) {
+ 
+   INCs <- getINCs(RGsetEx)
+   head(INCs)
+   dim(INCs)
+ }
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
[1] 613   6
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>