## ----style, include=FALSE, results='hide'------------------------------------- BiocStyle::markdown() library(boot) library(fission) library(SummarizedExperiment) library(ROCpAI) ## ----installation, eval=FALSE------------------------------------------------- # devtools::install_github("juanpegarcia/ROCpAI") ## ---- echo=FALSE, include=FALSE, results='hide'------------------------------- data("fission") genes <- as.data.frame(cbind(strain <- colData(fission)$strain, t(assay(fission)[c("SPNCRNA.1080","SPAC186.08c","SPNCRNA.1420","SPCC70.08c","SPAC212.04c"),]))) colnames(genes) <- c("Strain", "Gene1", "Gene2", "Gene3", "Gene4", "Gene5" ) ## ----------------------------------------------------------------------------- genes ## ----------------------------------------------------------------------------- pointsCurve(genes[,1], genes[,2]) ## ----------------------------------------------------------------------------- resultMc <- mcpAUC(genes, low.value = 0, up.value = 0.25, plot=TRUE) resultMc ## ----------------------------------------------------------------------------- test.Mc<- assay(resultMc) test.Mc$St_pAUC ## ----------------------------------------------------------------------------- test.Mc$pAUC ## ----------------------------------------------------------------------------- resultsT <- tpAUC(genes, low.value = 0, up.value = 0.25, plot=TRUE) resultsT ## ----------------------------------------------------------------------------- test.tpAUC <- assay(resultsT) ## ----------------------------------------------------------------------------- test.tpAUC$St_pAUC ## ----------------------------------------------------------------------------- test.tpAUC$pAUC ## ---- warning='hide'---------------------------------------------------------- resultstboot<- tpAUCboot(genes,low.value = 0, up.value = 0.25) ## ---- echo='hide'------------------------------------------------------------- test.tpAUCboot <- assay(resultstboot) resultT <- t(as.data.frame(cbind(test.tpAUCboot$Tp_AUC,test.tpAUCboot$sd,test.tpAUCboot$lwr,test.tpAUCboot$upr))) colnames(resultT) <- c("Gene1", "Gene2", "Gene3", "Gene4", "Gene5") rownames(resultT) <- c("Tp_AUC","sd","lwr","upr") ## ----------------------------------------------------------------------------- resultT ## ---- warning='hide'---------------------------------------------------------- resultsMcboot <- mcpAUCboot(genes,low.value = 0, up.value = 0.25) ## ---- echo='hide', results='hide'--------------------------------------------- test.mcpAUCboot <- assay(resultsMcboot) resultMc <- t(as.data.frame(cbind(test.mcpAUCboot$MCp_AUC,test.mcpAUCboot$sd,test.mcpAUCboot$lwr,test.mcpAUCboot$upr))) colnames(resultMc) <- c("Gene1", "Gene2", "Gene3", "Gene4", "Gene5") rownames(resultMc) <- c("MCp_AUC","sd","lwr","upr") ## ----------------------------------------------------------------------------- resultMc ## ----sessionInfo, eval=TRUE--------------------------------------------------- sessionInfo()