## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ----library, message=FALSE--------------------------------------------------- library(ExperimentHub) ## ----ExperimentHub------------------------------------------------------------ eh = ExperimentHub() ## ----show--------------------------------------------------------------------- eh ## ----dataprovider------------------------------------------------------------- head(unique(eh$dataprovider)) ## ----species------------------------------------------------------------------ head(unique(eh$species)) ## ----rdataclass--------------------------------------------------------------- head(unique(eh$rdataclass)) ## ----alpine------------------------------------------------------------------- apData <- query(eh, "alpineData") apData ## ----show2-------------------------------------------------------------------- apData$preparerclass df <- mcols(apData) ## ----length------------------------------------------------------------------- length(eh) ## ----subset------------------------------------------------------------------- mm <- query(eh, "mus musculus") mm ## ----display, eval=FALSE------------------------------------------------------ # d <- display(eh) ## ----dm2---------------------------------------------------------------------- apData apData["EH166"] ## ----dm3---------------------------------------------------------------------- apData[["EH166"]] ## ----show-2------------------------------------------------------------------- eh ## ----snapshot----------------------------------------------------------------- snapshotDate(eh) ## ----possibleDates------------------------------------------------------------ pd <- possibleDates(eh) pd ## ----setdate, eval=FALSE------------------------------------------------------ # snapshotDate(ah) <- pd[1] ## ---- eval=FALSE-------------------------------------------------------------- # # # make sure you have permissions on the cache/files # # use at own risk # # # moveFiles<-function(package){ # olddir <- path.expand(rappdirs::user_cache_dir(appname=package)) # newdir <- tools::R_user_dir(package, which="cache") # dir.create(path=newdir, recursive=TRUE) # files <- list.files(olddir, full.names =TRUE) # moveres <- vapply(files, # FUN=function(fl){ # filename = basename(fl) # newname = file.path(newdir, filename) # file.rename(fl, newname) # }, # FUN.VALUE = logical(1)) # if(all(moveres)) unlink(olddir, recursive=TRUE) # } # # # package="ExperimentHub" # moveFiles(package) # ## ---- eval=FALSE-------------------------------------------------------------- # path.expand(rappdirs::user_cache_dir(appname="ExperimentHub")) ## ---- eval=FALSE-------------------------------------------------------------- # library(ExperimentHub) # oldcache = path.expand(rappdirs::user_cache_dir(appname="ExperimentHub")) # setExperimentHubOption("CACHE", oldcache) # eh = ExperimentHub(localHub=TRUE) # # ## removes old location and all resources # removeCache(eh, ask=FALSE) # # ## create the new default caching location # newcache = tools::R_user_dir("ExperimentHub", which="cache") # setExperimentHubOption("CACHE", newcache) # eh = ExperimentHub() ## ----sessionInfo-------------------------------------------------------------- sessionInfo()