## ----env, echo=FALSE------------------------------------------------------- library("BiocStyle") ## ----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, warning = FALSE------------------- opt <- svmOptimisation(object = hyperLOPIT2015, fcol = "markers", times = 3, verbose = FALSE) res <- svmClassification(object = hyperLOPIT2015, assessRes = opt) ## ----cutoff, eval = FALSE, echo = TRUE------------------------------------- # pRolocVis(object = res, app = "classify", fcol = "svm") ## ----score, eval=FALSE----------------------------------------------------- # mythreshold <- pRolocVis(object = res, app = "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, app = "compare")