## ----knitr, echo=FALSE, cache = FALSE----------------------------------------- library(knitr) library(rmarkdown) opts_chunk$set(cache = FALSE, fig.align = "center", fig.width = 7, fig.height = 5) ## ----netrc_req, echo = FALSE-------------------------------------------------- # This chunk is only useful for BioConductor checks and shouldn't affect any other setup if (!any(file.exists("~/.netrc", "~/_netrc"))) { labkey.netrc.file <- ImmuneSpaceR:::.get_env_netrc() labkey.url.base <- ImmuneSpaceR:::.get_env_url() } ## ----CreateConnection, cache=FALSE, message=FALSE----------------------------- library(ImmuneSpaceR) sdy269 <- CreateConnection(study = "SDY269") sdy269 ## ----getDataset--------------------------------------------------------------- sdy269$getDataset("hai") ## ----getDataset-filter, message = FALSE--------------------------------------- library(Rlabkey) myFilter <- makeFilter(c("gender", "EQUAL", "Female")) hai <- sdy269$getDataset("hai", colFilter = myFilter) ## ----getGEMatrix-------------------------------------------------------------- sdy269$getGEMatrix("SDY269_PBMC_LAIV_Geo") ## ----getGEMatrix-multiple----------------------------------------------------- sdy269$getGEMatrix(c("SDY269_PBMC_TIV_Geo", "SDY269_PBMC_LAIV_Geo")) ## ----getGEMatrix-summary------------------------------------------------------ gs <- sdy269$getGEMatrix("SDY269_PBMC_TIV_Geo", outputType = "summary", annotation = "latest") ## ----plotting----------------------------------------------------------------- sdy269$plot("hai") sdy269$plot("elisa") ## ----cross-connection--------------------------------------------------------- con <- CreateConnection("") ## ----cross-connection-print--------------------------------------------------- con ## ----cross-connection-qplot--------------------------------------------------- plotFilter <- makeFilter( c("cohort", "IN", "TIV 2010;TIV Group 2008"), c("study_time_collected", "EQUALS", "7") ) con$plot("elispot", filter = plotFilter) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()