Hello bioC users, as you can see below, this was posted over a year ago. Unfortunately I tried the same today and for some mysterious it is not working correctly any more. What I have is the same data.frame: > dat id flybasename_gene flybase_gene_id entrezgene 1 1616608_a_at Gpdh FBgn0001128 33824 2 1622892_s_at CG33057 FBgn0053057 318833 3 1622892_s_at mkg-p FBgn0035889 38955 4 1622893_at IM3 FBgn0040736 50209 5 1622894_at CG15120 FBgn0034454 37248 GOMF 1 carboxylesterase activity:hydrolase activity:3',5'-cyclic-nucleotide phosphodiesterase activity:protein binding: 2 nucleotide binding:protein binding:ATP binding:chaperone binding:ammonium transmembrane transporter activity 3 nucleotide binding:protein binding:ATP binding:chaperone binding:ammonium transmembrane transporter activity 4 aminopeptidase activity:metalloexopeptidase activity:hydrolase activity:manganese ion binding 5 protein binding What I would like to have is a second data frame with the GO categories as row names and the gene IDs to be put in each of the GO categories they belong to. like that: GO genes protein binding FBgn0001128 FBgn0053057 FBgn0035889 etc. ammonium transmembrane transporter activity FBgn0053057 FBgn0035889 hydrolayse activity FBgn0040736 FBgn0001128 Below is the script I used before, and as far as I can remember it did work very good: lst <- tapply(1:nrow(dat), dat$flybase_gene_id, function(x) dat[x,"GOMF"]) lst2 <- lapply(lst, function(x) unlist(strsplit(as.character(x), ":"))) unlst <- cbind(rep(names(lst2), sapply(lst2, length)), unlist(lst2, use.names = FALSE)) done <- tapply(1:nrow(unlst), unlst[,2], function(x) unlst[x,1]) done_df <- lapply(done, paste, collapse = ",") out <- data.frame(GO = names(done_df), FBgn = unlist(done_df)) But the result I am getting are not the GO categories, but a numbered list of the the number of gene IDs, which looks like that: > out GO FBgn 1 1 FBgn0040736 2 2 FBgn0001128 3 3 FBgn0035889,FBgn0053057 4 4 FBgn0034454 I would like to know if something was changed in the apply command structure to prevent the same results as before. I would appreciate your help. Thanks Assa > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base [[alternative HTML version deleted]]

On 08/29/2012 12:34 AM, Assa Yeroslaviz wrote: > Hello bioC users, > > as you can see below, this was posted over a year ago. Unfortunately I > tried the same today and for some mysterious it is not working correctly > any more. > What I have is the same data.frame: >> dat > id flybasename_gene flybase_gene_id entrezgene > 1 1616608_a_at Gpdh FBgn0001128 33824 > 2 1622892_s_at CG33057 FBgn0053057 318833 > 3 1622892_s_at mkg-p FBgn0035889 38955 > 4 1622893_at IM3 FBgn0040736 50209 > 5 1622894_at CG15120 FBgn0034454 37248 > > GOMF > 1 carboxylesterase activity:hydrolase activity:3',5'-cyclic- nucleotide > phosphodiesterase activity:protein binding: > 2 nucleotide binding:protein binding:ATP binding:chaperone > binding:ammonium transmembrane transporter activity > 3 nucleotide binding:protein binding:ATP binding:chaperone > binding:ammonium transmembrane transporter activity > 4 aminopeptidase activity:metalloexopeptidase > activity:hydrolase activity:manganese ion binding > 5 > protein binding > > What I would like to have is a second data frame with the GO categories as > row names and the gene IDs to be put in each of the GO categories they > belong to. like that: > > > GO genes > protein binding FBgn0001128 FBgn0053057 FBgn0035889 etc. > ammonium transmembrane transporter activity FBgn0053057 FBgn0035889 > hydrolayse activity FBgn0040736 FBgn0001128 > > > Below is the script I used before, and as far as I can remember it did work > very good: > > > lst <- tapply(1:nrow(dat), dat$flybase_gene_id, function(x) dat[x,"GOMF"]) > lst2 <- lapply(lst, function(x) unlist(strsplit(as.character(x), ":"))) > > unlst <- cbind(rep(names(lst2), sapply(lst2, length)), unlist(lst2, > use.names = FALSE)) > done <- tapply(1:nrow(unlst), unlst[,2], function(x) unlst[x,1]) > done_df <- lapply(done, paste, collapse = ",") > out <- data.frame(GO = names(done_df), FBgn = unlist(done_df)) > > But the result I am getting are not the GO categories, but a numbered list > of the the number of gene IDs, which looks like that: > >> out > GO FBgn > 1 1 FBgn0040736 > 2 2 FBgn0001128 > 3 3 FBgn0035889,FBgn0053057 > 4 4 FBgn0034454 Probably GOMF is a factor, but was a character, dat$GOMF <- as.character(dat$GOMF) Here's a different code chunk, using Biobase::reverseSplit map <- with(dat, strsplit(setNames(GOMF, flybase_gene_id), ":")) revmap <- sapply(reverseSplit(map), paste, collapse=",") data.frame(GO=names(revmap), FBgn = as.vector(revmap)) Martin > > I would like to know if something was changed in the apply command > structure to prevent the same results as before. I would appreciate your > help. > > Thanks > Assa > >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793