inst/doc/getDataset.R

In ImmuneSpaceR: A Thin Wrapper around the ImmuneSpace Database

## ----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()