## ----knitr, echo = FALSE------------------------------------------------------ library(knitr) opts_chunk$set(echo = TRUE, cache = FALSE) ## ----netrc_req, echo = FALSE-------------------------------------------------- # This chunk is only useful for BioConductor checks and shouldn't affect any other setup if (!any(file.exists("~/.netrc", "~/_netrc"))) { labkey.netrc.file <- ImmuneSpaceR:::.get_env_netrc() labkey.url.base <- ImmuneSpaceR:::.get_env_url() } ## ----CreateConection, cache=FALSE, message = FALSE---------------------------- library(ImmuneSpaceR) sdy269 <- CreateConnection("SDY269") all <- CreateConnection("") ## ----listDatasets------------------------------------------------------------- sdy269$listDatasets() ## ----listDatasets-which------------------------------------------------------- all$listDatasets(output = "expression") ## ----getGEMatrix-------------------------------------------------------------- TIV_2008 <- sdy269$getGEMatrix("SDY269_PBMC_TIV_Geo") TIV_2011 <- all$getGEMatrix(matrixName = "SDY144_Other_TIV_Geo") ## ----ExpressionSet------------------------------------------------------------ TIV_2008 ## ----getGEMatrix-cohorts------------------------------------------------------ LAIV_2008 <- sdy269$getGEMatrix(cohortType = "LAIV group 2008_PBMC") ## ----summary------------------------------------------------------------------ TIV_2008_sum <- sdy269$getGEMatrix("SDY269_PBMC_TIV_Geo", outputType = "summary", annotation = "latest") ## ----summary-print------------------------------------------------------------ TIV_2008_sum ## ----multi-------------------------------------------------------------------- # Within a study em269 <- sdy269$getGEMatrix(c("SDY269_PBMC_TIV_Geo", "SDY269_PBMC_LAIV_Geo")) # Combining across studies TIV_seasons <- all$getGEMatrix(c("SDY269_PBMC_TIV_Geo", "SDY144_Other_TIV_Geo"), outputType = "summary", annotation = "latest") ## ----caching-dataset---------------------------------------------------------- names(sdy269$cache) ## ----caching-reload----------------------------------------------------------- TIV_2008 <- sdy269$getGEMatrix("SDY269_PBMC_TIV_Geo", reload = TRUE) ## ----caching-clear------------------------------------------------------------ sdy269$clearCache() ## ----sessionInfo-------------------------------------------------------------- sessionInfo()