Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../vignettes/pRolocGUI/inst/doc/pRolocGUI.R below:
## ----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") ## ----compare, eval = FALSE, echo = TRUE--------------------------------------- # data(hyperLOPIT2015ms3r1) # data(hyperLOPIT2015ms3r2) # mydata <- MSnSetList(list(hyperLOPIT2015ms3r1, hyperLOPIT2015ms3r2)) # pRolocVis(mydata, app = "compare", fcol = "markers") ## ----compare2, eval=FALSE, echo=TRUE------------------------------------------ # data("hyperLOPITU2OS2018") # data("lopitdcU2OS2018") # xx <- MSnSetList(list(hyperLOPITU2OS2018, lopitdcU2OS2018)) # if (interactive()) { # pRolocVis(xx, app = "compare", fcol = c("markers", "final.assignment")) # } ## ----aggvar, eval = FALSE, echo = TRUE, message = FALSE, warning = FALSE------ # ## load PSM data # data("hyperLOPIT2015ms2psm") # # ## Visualise the PSMs per to protein group # pRolocVis(hyperLOPIT2015ms2psm, app = "aggregate", fcol = "markers", # groupBy = "Protein.Group.Accessions") ## ----aggvar2, eval = FALSE, echo = TRUE, message = FALSE, warning = FALSE----- # ## Combine PSM data to peptides # hl <- combineFeatures(hyperLOPIT2015ms2psm, # groupBy = fData(hyperLOPIT2015ms2psm)$Sequence, # method = median) # # ## Visualise peptides according to protein group # pRolocVis(hyperLOPIT2015ms2psm, app = "aggregate", fcol = "markers", # groupBy = "Protein.Group.Accessions")
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