## @knitr include=FALSE library(GOSemSim) library(org.Hs.eg.db) library(GO.db) library(knitr) opts_chunk$set(tidy=TRUE,tidy.opts=list(keep.blank.line=FALSE, width.cutoff=50),out.truncate=80,out.lines=6,cache=TRUE,dev='pdf',include=TRUE,fig.width=6,fig.height=6,resolution=150) ## @knitr options,results='hide',echo=FALSE options(digits=3, width=80, prompt=" ", continue=" ") ## @knitr loading, eval=FALSE, results='hide' ## library(GOSemSim) ## help(GOSemSim) ## @knitr mgoSim goSim("GO:0004022", "GO:0005515", ont="MF", measure="Wang") go1 = c("GO:0004022","GO:0004024","GO:0004174") go2 = c("GO:0009055","GO:0005515") mgoSim(go1, go2, ont="MF", measure="Wang", combine=NULL) mgoSim(go1, go2, ont="MF", measure="Wang", combine="BMA") ## @knitr mgeneSim geneSim("241", "251", ont="MF", organism="human", measure="Wang", combine="BMA") mgeneSim(genes=c("835", "5261","241", "994"), ont="MF", organism="human", measure="Wang", verbose=FALSE) ## @knitr clusterSim, eval=F gs1 <- c("835", "5261","241", "994", "514", "533") gs2 <- c("578","582", "400", "409", "411") clusterSim(gs1, gs2, ont="MF", organism="human", measure="Wang", combine="BMA") x <- org.Hs.egGO hsEG <- mappedkeys(x) set.seed <- 123 clusters <- list(a=sample(hsEG, 20), b=sample(hsEG, 20), c=sample(hsEG, 20)) mclusterSim(clusters, ont="MF", organism="human", measure="Wang", combine="BMA") ## @knitr sessInfo, results='asis', echo=FALSE toLatex(sessionInfo())