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DSMolgenisArmadillo

Relevant for:

Use DSMolgenisArmadillo to analyse data shared in MOLGENIS Armadillo servers using DataSHIELD. DataSHIELD allows execution of a subset of analysis methods available in R. Methods such as:

ds.mean() ds.glm() ds.lmerSLMA()

For more detailed information please visit DSMolgenisArmadillo and additionally check the documentation: https://cran.datashield.org/.

Example
Prerequisite.r
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install.packages("DSI")
install.packages("DSMolgenisArmadillo")
install.packages("dsBaseClient", repos = c("http://cran.datashield.org", "https://cloud.r-project.org/"), dependencies = TRUE)

library(dsBaseClient)
library(DSMolgenisArmadillo)
Example
Analyse_data_subset_DSMolgenisArmadillo.r
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library(dsBaseClient)
library(DSMolgenisArmadillo)

# specify server url
armadillo_url <- "https://armadillo.test.molgenis.org"

# get token from central authentication server
token <- armadillo.get_token(armadillo_url)


# build the login dataframe
builder <- DSI::newDSLoginBuilder()
builder$append(
    server = "armadillo",
    url = armadillo_url,
    token = token,
    table = "workshop1/2_1-core-1_0/nonrep",
    driver = "ArmadilloDriver"
)

# create loginframe
logindata <- builder$build()

# login into server
conns <- datashield.login(
    logins = logindata, 
    symbol = "core_nonrep", 
    variables = c("coh_country"), 
    assign = TRUE
)

# calculate the mean
ds.mean("core_nonrep$coh_country", datasources = conns)

ds.histogram(x = "core_nonrep$coh_country", datasources = conns)

Info

A researcher only has access to data if he/she has been granted access to this data (typically) by a data manager or administrator of a cohorts Armadillo server.

Note

The example files used in the examples above can be found here: nonrep.parquet, yearlyrep.parquet

Load these parquet files in R and see which variables you can call.