GOSemSim redesign in terms of S4 classes
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I started to develop GOSemSim package two years ago when I was not quite familiar with R. I am very happy to see that someone use it and found it helpful.
I try to learn S4 and redesign GOSemSim with S4 classes and methods in the pass two weeks, and the very first version was implemented. As I’m not very familiar with S4, the package may need improve in many aspect.
The newest version of GOSemSim can be installed by:
install.packages("GOSemSim",repos="http://www.bioconductor.org/packages/devel/bioc",type="source")
Here come some example:
> library(GOSemSim) Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: GO.db Loading required package: DBI Loading required package: org.Hs.eg.db > params <- new("Params", ontology="MF", organism="human", method="Wang") > > > go1 <- c("GO:0004022", "GO:0004024", "GO:0004023") > go2 <- c("GO:0009055", "GO:0020037") > gos <- new("GOIdentifiers", GOSet1=go1, GOSet2=go2) > > gs1 <- c("835", "5261","241", "994", "514", "533") > gs2 <- c("578","582", "400", "409", "411") > gs <- new("GeneIdentifiers", GeneSet1=gs1, GeneSet2=gs2) > > x <- org.Hs.egGO > hsEG <- mappedkeys(x) > clusters <- list(a=sample(hsEG, 20), b=sample(hsEG, 20), c=sample(hsEG, 20)) > geneClusters <- new("GeneClusterSet", GeneClusters=clusters) > > sim(gos,params) GO:0009055 GO:0020037 GO:0004022 0.318 0.151 GO:0004024 0.290 0.136 GO:0004023 0.290 0.136 > setCombineMethod(params)<-"rcmax.avg" > sim(gos,params) [1] 0.273 > sim(gs, params) [1] "loading GOMap..." [1] "Done..." 578 582 400 409 411 835 0.743 1.000 0.624 0.741 0.543 5261 0.551 0.842 0.580 0.582 0.438 241 0.729 1.000 0.666 0.702 0.360 994 0.610 1.000 0.542 0.642 0.673 514 0.285 0.390 0.420 0.282 0.550 533 0.378 0.481 0.373 0.369 0.357 > sim(geneClusters, params) a b c a 1.000 0.782 0.770 b 0.782 1.000 0.745 c 0.770 0.745 1.000 > > setOrganism(params) <- "yeast" Loading required package: org.Sc.sgd.db [1] "loading GOMap..." [1] "Done..." > ygs <- new("GeneIdentifiers", GeneSet1="snR18", GeneSet2="YPR062W") > sim(ygs,params) [1] 0.199 > setOntology(params) <- "BP" > sim(ygs,params) [1] 0.295 > setMethod(params) <- "Resnik" > sim(ygs,params) [1] 0.234
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