Genes2GO and suggestions to make it faster
Konika Chawla <[email protected]>
| Newsgroups | gmane.science.biology.informatics.conductor |
|---|---|
| Message-ID | <[email protected]> |
Hi,
I have created this webapp
(http://norstore-trd-bio0.hpc.ntnu.no:8080/Genes2GO/clearpage.do) to
makes a binary matrix between user specified genes and user selected GO
term to represent the gene annotations by either 1 or 0. Users can also
specify just some query terms and the program will find the related GO
terms.
Its small and useful tool for biologists.
The tools uses annotation data from biomaRt and GO.DB to find GO terms.
1) The tool is bit slow sometimes. Any suggestion to make it faster
would be helpful.
A small part of code is
"ensembl = useMart("ensembl", dataset = organism)
godata<-getBM(attributes = c(list_type,"go_id","name_1006"), filters =
list_type, values = genelist[,1], mart = ensembl)
godata<-trim(as.matrix(godata))"
2) Is it possible to show a progress bar on the webpage which could
represent how much time is remaining to finish the process. That is if
we can know how much time the process is going to take.
Thanks is advance.
--
With Regards,
Konika Chawla
NTNU, Norway
Phone +4772821344
_______________________________________________
Bioconductor mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor