## ----style, echo=FALSE, results="asis", message=FALSE-------------------- knitr::opts_chunk$set(tidy = FALSE, warning = FALSE, message = FALSE) CRANpkg <- function (pkg) { cran <- "https://CRAN.R-project.org/package" fmt <- "[%s](%s=%s)" sprintf(fmt, pkg, cran, pkg) } Biocpkg <- function (pkg) { sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg) } ## ----echo=FALSE, results='hide', message=FALSE--------------------------- library(DOSE) ## ------------------------------------------------------------------------ a <- c("DOID:14095", "DOID:5844", "DOID:2044", "DOID:8432", "DOID:9146", "DOID:10588", "DOID:3209", "DOID:848", "DOID:3341", "DOID:252") b <- c("DOID:9409", "DOID:2491", "DOID:4467", "DOID:3498", "DOID:11256") doSim(a[1], b[1], measure="Wang") doSim(a[1], b[1], measure="Resnik") doSim(a[1], b[1], measure="Lin") s <- doSim(a, b, measure="Wang") s ## ------------------------------------------------------------------------ simplot(s, color.low="white", color.high="red", labs=TRUE, digits=2, labs.size=5, font.size=14, xlab="", ylab="") ## ----warning=FALSE------------------------------------------------------- g1 <- c("84842", "2524", "10590", "3070", "91746") g2 <- c("84289", "6045", "56999", "9869") geneSim(g1[1], g2[1], measure="Wang", combine="BMA") gs <- geneSim(g1, g2, measure="Wang", combine="BMA") gs ## ------------------------------------------------------------------------ clusterSim(g1, g2, measure="Wang", combine="BMA") ## ------------------------------------------------------------------------ g3 <- c("57491", "6296", "51438", "5504", "27319", "1643") clusters <- list(a=g1, b=g2, c=g3) mclusterSim(clusters, measure="Wang", combine="BMA")