## ---- echo=FALSE, results='hide', eval=FALSE---------------------------------- # library(knitr) # opts_knit$set(cache=TRUE) ## ---- echo=FALSE, message=FALSE----------------------------------------------- library(doppelgangR) ## ---- message = FALSE--------------------------------------------------------- library(curatedOvarianData) data(GSE32062.GPL6480_eset) data(GSE17260_eset) ## ----testesets---------------------------------------------------------------- testesets <- list(JapaneseA=GSE32062.GPL6480_eset, Yoshihara2010=GSE17260_eset) ## ----rundopp, results="hide", message=FALSE, cache=TRUE----------------------- results1 <- doppelgangR(testesets, phenoFinder.args=NULL) ## ----summarizedop, results='hide'--------------------------------------------- summary(results1) ## ----plotdop, fig.cap="Doppelgängers identified on the basis of similar expression profiles. The vertical red lines indicate samples that were flagged."---- par(mfrow=c(2,2), las=1) plot(results1) ## ----------------------------------------------------------------------------- plot(results1, plot.pair=c("JapaneseA", "JapaneseA")) ## ----rundopp2, results="hide", message=FALSE, eval=FALSE---------------------- # results1 <- doppelgangR(testesets, # outlierFinder.expr.args = list(bonf.prob = 1.0, transFun = atanh, # tail = "upper")) ## ----------------------------------------------------------------------------- mat <- matrix(1:4, ncol=2) library(Biobase) eset <- ExpressionSet(mat) class(eset) ## ---- eval=FALSE-------------------------------------------------------------- # results2 <- doppelgangR(testesets, BPPARAM = MulticoreParam(workers = 8))