[BioC] annotate htmlpage error

[Georg Otto]

"James W. MacDonald" <jmacdon at uw.edu> writes:

> Hi Martin,
>
> On 3/14/2012 4:36 PM, Martin Morgan wrote:
>> On 03/14/2012 01:13 PM, Georg Otto wrote:
>>> Hi,
>>>
>>> after updating the annotate package from 1.32.1 to 1.32.2 I get an error
>>> using the htmlpage function. Here with the old version:
>>
>> Sorry, probably my fault; I've tried to update this in v. 1.32.3. If
>> you provide a fully reproducible example (deg$id, othernames,
>> table.head as necessary to reproduce just the bug) I could be more
>> sure of the fix. Martin
>
> library(annotate)
> library(org.Hs.eg.db)
> gnlst2 <- list(egs = head(Rkeys(org.Hs.egENSEMBL),3))
> example(htmlpage)
> htmlpage(gnlst2, "test.html","Some gene expression data", otherdata,
> c("Ens", table.head[-c(1:3)]), repository=list("ens"), species =
> "Homo_sapiens")
>
>

Thanks Jim. I can confirm tah Martin's fix works. However it generates a
dead link. In getQuery4ENSEMBL() the link is created like this:

out <- paste("http://www.ensembl.org/", species, "/Search/Summary?species=",
                 species, ";idx=;q=", ids, sep = "")
 
However (dependant on where you exactly want to point the link to) it
should read like this:

out <- paste("http://www.ensembl.org/", species, "/Gene/Summary?g=",
                 ids, sep = "")


Best,

Georg