[BioC] string to function argument

Jeremiah H. Savage jeremiahsavage at gmail.com
Wed Jun 30 04:17:39 CEST 2010

Hi Sean,

I just saw your message after sending the last one a minute ago.

My question was that I wanted to use a character object 'gplaccess'
that contained the string "gpldata$GPL96"

I wanted to use this string to access a data.frame in a GEOData
object, but the Table() function expects a GEOData-Class, not a

So Table(gpldata$GPL96) will access the data.frame but
Table(gplaccess) would not access that data.frame, as I get the following error:

> Table(gplaccess)
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "Table", for
signature "character"

So, is there a function I can apply to 'gplaccess' to have it be an
accepted argument to Table()?  I tried     Table(cat(gplaccess))
Table(as.name(gplaccess))        and others without success.

Thanks again,

On Tue, Jun 29, 2010 at 6:47 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> Hi, Jeremiah.
> The gpldata object is a list and the line that you are using that you say
> does work is the correct way to access the data.  I'm not sure what else you
> are trying to do.  Could you clarify?
> Sean
> On Jun 29, 2010 7:44 PM, "Jeremiah H. Savage" <jeremiahsavage at gmail.com>
> wrote:
> Hello,
> I would like to get the Table information out of multiple GPLList objects.
> How can I use a string/char variable as a function argument?
> In this case the function is GEOquery::Table()
> geodata <- parseGEO("GSExxxx.soft")
> gpldata <- GPLList(geodata)[1]
> gplname <- names(gpldata)  # eg. "GPL96"
> gplaccess <- paste(gpldata,gplname,sep="$")
> ENTREZ_GENE_ID <- Table(gplaccess)$ENTREZ_GENE_ID
> ###^^^ the above line does NOT work ,but
> ###^^^ the above line DOES work
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