[BioC] LocusLink now redirects to Entrez Gene

[James W. MacDonald]

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
> 


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623