inst/doc/vignettes.R

In ROCpAI: Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers

## ----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"  )


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genes 

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pointsCurve(genes[,1], genes[,2])

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resultMc <- mcpAUC(genes, low.value = 0, up.value = 0.25, plot=TRUE)
resultMc

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test.Mc<- assay(resultMc)
test.Mc$St_pAUC

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test.Mc$pAUC

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resultsT <- tpAUC(genes, low.value = 0, up.value = 0.25, plot=TRUE)
resultsT

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test.tpAUC <- assay(resultsT)


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test.tpAUC$St_pAUC


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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")

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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")

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resultMc

## ----sessionInfo, eval=TRUE---------------------------------------------------
sessionInfo()