array2ade4 {made4} | R Documentation |
Converts input data into a data.frame suitable for analysis
in ADE4. This function is called by bga
and other made4
function.
array2ade4(dataset, pos = FALSE, trans = FALSE)
dataset |
A matrix , data.frame ,
exprSet or marrayRaw .
If the input is gene expression data in a matrix or data.frame . The
rows and columns are expected to contain the variables (genes) and cases (array samples)
respectively.
|
pos |
Logical indicating whether to add an integer to dataset , to generate positive data.frame . Required for
dudi.coa or dudi.nsc |
trans |
Logical indicating whether dataset should be transposed. Default is FALSE |
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
,
exprSet
or marrayRaw
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()).
Returns a data.frame suitable for analysis by ade4 or made4 functions.
Aedin Culhane
library(affy) data(geneData) class(geneData) dim(geneData) dim(array2ade4(geneData)) class(array2ade4(geneData))