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Question: Genes2GO and suggestions to make it faster
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gravatar for Konika Chawla
4.2 years ago by
Konika Chawla20 wrote:
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
ADD COMMENTlink modified 4.2 years ago by Sean Davis21k • written 4.2 years ago by Konika Chawla20
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gravatar for Sean Davis
4.2 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Mon, Aug 18, 2014 at 8:52 AM, Konika Chawla <chawla at="" ntnu.no=""> wrote: > 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))" > I'd suggest eliminating the biomaRt call in the webapp. Simply use biomaRt to get all results for all genes and then do the filtering in R. The call to biomaRt will almost certainly be the most time-consuming process. > > 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. As written above, that probably will not be possible. In general, to make a progress bar, you'll need to be able to measure progress somehow and that really isn't possible with biomaRt. Sean [[alternative HTML version deleted]]
ADD COMMENTlink written 4.2 years ago by Sean Davis21k
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