## ----knitr, echo=FALSE, cache = FALSE------------------------------------ library(knitr) library(rmarkdown) opts_chunk$set(cache = FALSE) ## ----netrc_req, echo = FALSE--------------------------------------------- # This chunk is only useful for BioConductor checks and shouldn't affect any other setup if (!any(file.exists("~/.netrc", "~/_netrc"))) { labkey.netrc.file <- ImmuneSpaceR:::get_env_netrc() labkey.url.base <- ImmuneSpaceR:::get_env_url() } ## ----CreateConnection, cache=FALSE, message=FALSE------------------------ library(ImmuneSpaceR) sdy269 <- CreateConnection(study = "SDY269") sdy269 ## ----getDataset---------------------------------------------------------- sdy269$getDataset("hai") ## ----getDataset-filter, message = FALSE---------------------------------- library(Rlabkey) myFilter <- makeFilter(c("gender", "EQUAL", "Female")) hai <- sdy269$getDataset("hai", colFilter = myFilter) ## ----getGEMatrix--------------------------------------------------------- sdy269$getGEMatrix("LAIV_2008") ## ----getGEMatrix-multiple------------------------------------------------ sdy269$getGEMatrix(c("TIV_2008", "LAIV_2008")) ## ----getGEMatrix-summary------------------------------------------------- gs <- sdy269$getGEMatrix("TIV_2008", outputType = "summary", annotation = "latest") ## ---- dev='png', fig.width=15-------------------------------------------- sdy269$plot("hai") sdy269$plot("elisa") ## ---- cross-connection--------------------------------------------------- con <- CreateConnection("") ## ---- cross-connection-print--------------------------------------------- con ## ----cross-connection-qplot, dev='png', fig.align="center"--------------- plotFilter <- makeFilter(c("cohort", "IN", "TIV 2010;TIV Group 2008")) con$plot("elispot", filter = plotFilter) ## ----sessionInfo--------------------------------------------------------- sessionInfo()