## ----knitr, echo = FALSE------------------------------------------------------ library(knitr) opts_chunk$set(echo = TRUE) ## ----netrc_req, echo = FALSE-------------------------------------------------- # This chunk is only useful for BioConductor checks and shouldn't affect any other setup if (!any(file.exists("~/.netrc", "~/_netrc"))) { labkey.netrc.file <- ImmuneSpaceR:::.get_env_netrc() labkey.url.base <- ImmuneSpaceR:::.get_env_url() } ## ----CreateConection, cache=FALSE, message=FALSE------------------------------ library(ImmuneSpaceR) sdy269 <- CreateConnection("SDY269") all <- CreateConnection("") ## ----listDatasets------------------------------------------------------------- sdy269$listDatasets() all$listDatasets() ## ----getDataset--------------------------------------------------------------- hai_269 <- sdy269$getDataset("hai") hai_all <- all$getDataset("hai") head(hai_269) ## ----makeFilters, cache = FALSE----------------------------------------------- library(Rlabkey) # Get participants under age of 30 young_filter <- makeFilter(c("age_reported", "LESS_THAN", 30)) # Get a specific list of two participants pid_filter <- makeFilter(c("participantid", "IN", "SUB112841.269;SUB112834.269")) ## ----filters------------------------------------------------------------------ # HAI data for participants of study SDY269 under age of 30 hai_young <- sdy269$getDataset("hai", colFilter = young_filter) # List of participants under age 30 demo_young <- all$getDataset("demographics", colFilter = young_filter) # ELISPOT assay results for two participants mbaa_pid2 <- all$getDataset("elispot", colFilter = pid_filter) ## ----views-------------------------------------------------------------------- full_hai <- sdy269$getDataset("hai", original_view = TRUE) colnames(full_hai) ## ----caching-dataset---------------------------------------------------------- pcr <- sdy269$getDataset("pcr") names(sdy269$cache) ## ----caching-views------------------------------------------------------------ pcr_ori <- sdy269$getDataset("pcr", original_view = TRUE) names(sdy269$cache) ## ----caching-reload----------------------------------------------------------- hai_269 <- sdy269$getDataset("hai", reload = TRUE) ## ----caching-clear------------------------------------------------------------ sdy269$clearCache() names(sdy269$cache) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()