[BioC] LocusLink now redirects to Entrez Gene

[Ramsi Haddad]

Thanks!

Ramsi

On Thu, 2005-03-10 at 15:20, James W. MacDonald wrote:
> Ramsi Haddad wrote:
> > Dear List,
> > 
> > 	I have been using the function htmlpage() from the annotate package. 
> > It used to be called ll.htmlpage().  It generates an html page with
> > hotlinks to LocusLink.  Now I click a link, the locuslink page tells me
> > its closed and that I'll be redirected to Gene.  I've looked at the code
> > and it referred to a function getQueryLink().  this last function does
> > not have an entry for Entrez Gene.  Has anyone else dealt with this
> > problem?  Thanks for your assistance.
> 
> The fix for this is relatively simple, but unfortunately will not be 
> propagated to the release version until April or so, when the new BioC 
> release occurs.
> 
> A simple fix is to replace the function getQuery4LL() with this:
> 
> getQuery4LL <- function (ids)
> {
>      if (is.factor(ids)) {
>          options(warn = -1)
>          ids <- as.numeric(as.character(ids))
>          options(warn = 0)
>          blanks <- is.na(ids)
>      }
>      if (is.character(ids)) {
>          options(warn = -1)
>          ids <- as.numeric(ids)
>          options(warn = 0)
>          blanks <- is.na(ids)
>      }
>      if (is.numeric(ids))
>          blanks <- is.na(ids)
>      out <- vector()
>      for (i in seq(along = ids)) {
>          if (!blanks[i])
>              out[i] <- 
> paste("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=", 
> 
>                  ids[i], sep = "")
>          else out[i] <- "&nbsp;"
>      }
>      return(out)
> }
> 
> HTH,
> 
> Jim
> 
> 
> > 
> > Ramsi
> > 
>