[BioC] ReportingTools - trouble incorporating annotations

[James W. MacDonald]

Hi Sam,

On 6/19/2013 6:17 PM, Sam McInturf wrote:
> Finally, some of my annotations have a one to many mapping which 
> results in one gene being displayed on several lines with the only 
> change being in one field (say, PMIDs).  Is there a 'fast' way to put 
> all of these many to one mappings into a a single deliminated field 
> (18614708 / 18614708 / 18614708) or is it something that I should just 
> make a quick function for?

I usually do this sort of thing with a combination of the Xapply family 
of functions.

annot <- select(org.At.tair.db, keys= rownames(tempDE$genes), col = 
c("SYMBOL", "PMID", "GENENAME"), keytype="TAIR")

annotlst <- tapply(seq_len(nrow(annot)), annot[,1], function(x) annot[x,])
annotlst <- do.call("rbind", lapply(annotlst, function(x) t(apply(x, 2, 
function(y) paste(unique(y), collapse = "/")))))

Best,

Jim


-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099