On Wed, Nov 23, 2011 at 2:29 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 11/22/2011 02:33 PM, Biase, Fernando Henrique wrote: > >> Hi everyone, >> >> Is there a way to retrieve the level for a GO category in R? >> >> As of now I am retrieving terms by using the following code: >> >> BP_terms<- stack(lapply(mget(GO_BP_Cats_**5_more_genes$category, >>> GOTERM, ifnotfound=NA), Term)) >>> >> >> Now I wanted go get the level (3,4,5...,9). >> >> I looked into the "annotate" package and the " .db" (I am using >> org.Bt.eg.db) usage but could not find it. >> >> Any hint would be very much appreciated. >> > > Hi, > > Maybe using the CHILDREN (immediate descendants) or OFFSPRING maps ? For > instance > > > toTable(GOBPCHILDREN["GO:**0071842"]) > go_id go_id RelationshipType > 1 GO:0006323 GO:0071842 is_a > 2 GO:0006996 GO:0071842 is_a > 3 GO:0007028 GO:0071842 is_a > 4 GO:0030030 GO:0071842 is_a > 5 GO:0034621 GO:0071842 is_a > 6 GO:0034994 GO:0071842 is_a > 7 GO:0035845 GO:0071842 is_a > 8 GO:0043062 GO:0071842 is_a > 9 GO:0043580 GO:0071842 is_a > 10 GO:0071844 GO:0071842 is_a > 11 GO:0071845 GO:0071842 is_a > 12 GO:0071956 GO:0071842 is_a > 13 GO:0072553 GO:0071842 is_a > 14 GO:0097061 GO:0071842 is_a > > or > > > length(mappedLkeys(**GOBPOFFSPRING["GO:0071842"])) > [1] 1683 > > The 'Lkeys' could be retrieved recursively, or to find out more > information about the terms > > > toTable(GOTERM[mappedLkeys(**GOBPCHILDREN["GO:0071842"])]) > > If you want to do something more than enumerate the children, perhaps the > graph package would be appropriate. > I had a look at makeGOGraph in GOstats. We can run the example and then use RBGL's sp.between to get a path > example(makeGOGraph) mkGOGr> library("hgu95av2.db") mkGOGr> set.seed(321) mkGOGr> uniqun <- function(x) unique(unlist(x)) mkGOGr> gN <- uniqun(sample(hgu95av2ENTREZID, 4)) mkGOGr> gg1 <- makeGOGraph(gN, "BP", chip="hgu95av2.db") > sp.between(gg1, "GO:0006366", "GO:0008150") $`GO:0006366:GO:0008150` $`GO:0006366:GO:0008150`$length [1] 5 $`GO:0006366:GO:0008150`$path_detail [1] "GO:0006366" "GO:0006351" "GO:0010467" "GO:0043170" "GO:0008152" [6] "GO:0008150" $`GO:0006366:GO:0008150`$length_detail $`GO:0006366:GO:0008150`$length_detail[[1]] GO:0006366->GO:0006351 GO:0006351->GO:0010467 GO:0010467->GO:0043170 1 1 1 GO:0043170->GO:0008152 GO:0008152->GO:0008150 1 1 However when I tried to get the mapfun parameter to work with the org.Bt.eg.db mappings, I came a-cropper. Some of the doc on the GOstats makeGOGraph man page seems to be out of date. A little programming with org.* and GO.db will probably yield a general method. > sessionInfo() R Under development (unstable) (2011-11-15 r57665) Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) locale: [1] en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US .US-ASCII attached base packages: [1] grid stats graphics grDevices datasets utils tools [8] methods base other attached packages: [1] Rgraphviz_1.33.0 RBGL_1.31.1 GO.db_2.6.1 [4] hgu95av2.db_2.6.3 org.Hs.eg.db_2.6.4 GOstats_2.21.0 [7] RSQLite_0.10.0 DBI_0.2-5 graph_1.33.0 [10] Category_2.21.0 AnnotationDbi_1.17.4 Biobase_2.15.1 [13] BiocGenerics_0.1.3 BiocInstaller_1.3.3 weaver_1.21.0 [16] codetools_0.2-8 digest_0.5.1 loaded via a namespace (and not attached): [1] annotate_1.33.0 genefilter_1.37.0 GSEABase_1.17.1 IRanges_1.13.8 [5] splines_2.15.0 survival_2.36-10 XML_3.4-3 xtable_1.6-0 > > Hope that helps, > > Martin > > >> Thanks in advance, Fernando >> >> >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ Bioconductor mailing >> list Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor="">Search the >> archives: >> http://news.gmane.org/gmane.**science.biology.informatics.**conduct or<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: M1-B861 > Telephone: 206 667-2793 > > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]