Converts microarray input data into a data frame suitable for analysis in ADE4.

Description

Converts input data into a data.frame suitable for analysis in ADE4. This function is called by bga and other made4 function.

Usage

array2ade4(dataset, pos = FALSE, trans = FALSE)

Arguments

Details

bga and other functions in made4 call this function and it is generally not necessary to call array2ade4 this directly.

array2ade4 calls getdata, and will accept a matrix, data.frame, ExpressionSet or marrayRaw-class format. It will also transpose data or add a integer to generate a positive data matrix.

If the input data contains missing values (NA), these must first be removed or imputed (see the R libraries impute() or pamr()).

Value

Returns a data.frame suitable for analysis by ade4 or made4 functions.

Author(s)

Aedin Culhane

See Also

getdata,as in the Bioconductor package convert.

Examples

library(affy)
data(geneData)
class(geneData)
dim(geneData)
dim(array2ade4(geneData))
class(array2ade4(geneData))

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 'demo()' for some demos, 'help()' for on-line help, or
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> library(made4)
Loading required package: ade4
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: scatterplot3d
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/made4/array2ade4.Rd_%03d_medium.png", width=480, height=480)
> ### Name: array2ade4
> ### Title: Converts microarray input data into a data frame suitable for
> ###   analysis in ADE4.
> ### Aliases: array2ade4
> ### Keywords: manip
> 
> ### ** Examples
> 
> library(affy)
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 object is masked from 'package:ade4':

    score

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")'.

> data(geneData)
> class(geneData)
[1] "matrix"
> dim(geneData)
[1] 500  26
> dim(array2ade4(geneData))
[1] 500  26
> class(array2ade4(geneData))
[1] "data.frame"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>