## ----loadPkgs, message = FALSE, warning = FALSE--------------------------
library("pRolocGUI")
library("pRolocdata")

## ----loadData, echo = TRUE, message = FALSE, warning = FALSE-------------
data(hyperLOPIT2015) 

## ----example, eval = FALSE, echo = TRUE----------------------------------
## pRolocVis(object = hyperLOPIT2015, fcol = "markers")

## ----pca1, eval = FALSE, echo = TRUE-------------------------------------
## pRolocVis(object = hyperLOPIT2015, fcol = "markers")

## ----classify, eval = TRUE, echo = TRUE----------------------------------
opt <- svmOptimisation(object = hyperLOPIT2015, 
                       fcol = "markers", 
                       times = 3, verbose = FALSE)
res <- svmClassification(object = hyperLOPIT2015, assessRes = opt) 

## ----cutoff, eval = FALSE, echo = TRUE-----------------------------------
## pRolocVis(object = res, what = "classify", fcol = "svm")

## ----score, eval=FALSE---------------------------------------------------
## mythreshold <- pRolocVis(object = res, what = "classify", fcol = "svm")
## res <- getPredictions(res, fcol = "svm",
##                       mcol = "markers", t = mythreshold)

## ----compare, eval = FALSE, echo = TRUE----------------------------------
## data(hyperLOPIT2015ms3r1)
## data(hyperLOPIT2015ms3r2)
## mydata <- MSnSetList(list(hyperLOPIT2015ms3r1, hyperLOPIT2015ms3r2))
## pRolocVis(mydata, what = "compare")