Give the option not to download GPL data

[renozao]

Would it be possible to add an argument to getGEO, e.g., GPLdata = TRUE, or define a special meaning for an NA value in AnnotGPL, that indicates if GPL feature data should be downloaded at all?

Example:

> eset <- getGEO('GSE12345')
> head(fData(eset)[, 1:5])
                 ID GB_ACC SPOT_ID Species Scientific Name Annotation Date
1007_s_at 1007_s_at U48705    <NA>            Homo sapiens     Jun 9, 2011
1053_at     1053_at M87338    <NA>            Homo sapiens     Jun 9, 2011
117_at       117_at X51757    <NA>            Homo sapiens     Jun 9, 2011
121_at       121_at X69699    <NA>            Homo sapiens     Jun 9, 2011
1255_g_at 1255_g_at L36861    <NA>            Homo sapiens     Jun 9, 2011
1294_at     1294_at L13852    <NA>            Homo sapiens     Jun 9, 2011
> 
> # while no feature data is fetched with:
> eset <- getGEO('GSE12345', GPLdata = FALSE)
> # or
> # eset <- getGEO('GSE12345', AnnotGPL = NA)
> featureData(eset)
An object of class 'AnnotatedDataFrame': none
> fData(eset)
data frame with 0 columns and 54675 rows

Note that one needs to be careful when setting an empty feature data AnnotatedDataFrame object: rownames must still correspond to featureNames, otherwise the object does not pass validation:

> featureData(eset) <- AnnotatedDataFrame(data.frame(row.names = featureNames(eset)))
> validObject(eset)
[1] TRUE
> featureData(eset) <- AnnotatedDataFrame()
> validObject(eset)
Error in validObject(eset) : 
  invalid class “ExpressionMix” object: 1: feature numbers differ between assayData and featureData
invalid class “ExpressionMix” object: 2: featureNames differ between assayData and featureData

Thanks!

[seandavi]

Hi, Renaud.

I think this should allow the functionality that you want. You can either checkout from here or install from the devel branch on bioc in a day or so after the build system has done its thing. I am closing, but feel free to reopen or simply put in a new issue if this doesn't meet your needs.

[renozao]

Thanks!