Dear Biocore Team (and users of GOstats):

It appears that the Sanger URL format has changed for the Pfam site, which causes broken links when using summary() with option htmlLinks=TRUE. Below is a comparison of the old and new URLs for the same accession number.

OLD
http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF07974

NEW
http://pfam.sanger.ac.uk/family?acc=PF07974

The latest development version of GOstats (2.17.1) that I looked at (below) shows the old form so I thought I would pass along.

Thanks for all your hard work with Bioconductor. It is greatly appreciated!


-------------------------------------------------------------------------

showMethods(summary, class = "PFAMHyperGResult", includeDefs = TRUE)

Function: summary (package base)
object="PFAMHyperGResult"
function (object, ...)
{
    .local <- function (object, pvalue = pvalueCutoff(object),
        categorySize = NULL, htmlLinks = FALSE)
    {
        PFAM_URL <- "http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?%s"
        df <- callNextMethod(object = object, pvalue = pvalue,
            categorySize = categorySize)
        if (nrow(df) == 0) {
            df$Term <- character(0)
            return(df)
        }
        pfamIds <- df[[1]]
        if (htmlLinks) {
            pfamIdUrls <- sapply(pfamIds, function(x) sprintf(PFAM_URL,
                x))
            pfamTerms <- paste("<a href=\"", pfamIdUrls, "\">",
                pfamIds, "</a>", sep = "")
        }
        else {
            pfamTerms <- pfamIds
        }
        df$Term <- pfamTerms
        df
    }
    .local(object, ...)
}


--------------------------------------------------------------------------


J. Wade Davis, PhD
Assistant Professor
187 Galena DC 018.0
University of Missouri
Columbia, MO 65212
Phone: (573) 882-0770
Fax: (573) 884-4196
MU Biostatistics Group<http://som.missouri.edu/Research/BioStat/Default.aspx>


	[[alternative HTML version deleted]]

