Create resources

In MolgenisArmadillo: Armadillo Client for the Armadillo Service

library(MolgenisArmadillo)

If you want to perform “omics”-like analyses you probably need to upload data (resources). By default Armadillo supports file uploads up to 500MB. If you need to upload larger resources, please contact [e-mail].

There are 2 roles you can assume using the package. The datamanager role and the researcher role.

Datamanager

The datamanager needs to make the data available to the researchers. Besides this you need to create the resources to access the data.

Researcher

The researcher can call DataSHIELD analysis methods on the data uploaded by the datamanager.

Upload the data

As a datamanager you need to access the Armadillo webinterface to be able to access the resource.

1. We are using data from the following sources:
2. https://github.com/isglobal-brge/brge_data_large/blob/master/data/gse66351_1.rda
3. https://github.com/isglobal-brge/brge_data_large/blob/master/data/gse66351_2.rda
4. Login with your institute account.
5. Create a project. For example omics.
6. Click on the edit project button to the right of the name of your project.
7. Create a new folder for your data. For example ewas.
8. Click on the "Select a file to upload" button or drag your file to upload to the box and click on "Upload". Upload the omics data.

Upload the resources (in Rstudio)

A second option to upload data (resources) is on the Central Analysis Server (CAS) within Rstudio As datamanager you first need to login to Armadillo (as superuser)

armadillo.login("https://armadillo-demo.molgenis.net/")
#> [1] "We're opening a browser so you can log in with code 92B64Y"

Install prerequisites

If you want to install a package on the Armadillo Rserver you can execute the following. The selected profile is always default if none is specified. If your profile doesn't have the resourcer package installed, install it:

library(resourcer)

Create resources

In order to be able to assign the data uploaded in the armadillo you need to create the resources as well. The data files you uploaded to armadillo, can be retrieved via the following URL: yoururl + /storage/projects/{project name}/objects/{folder name}%2F{filename} an example is: https://armadillo-demo.molgenis.net/storage/projects/omics/objects/ewas%2Fgse66351_1.rda. Here the URL is https://armadillo-demo.molgenis.net/, the project name is omics, the folder is ewas and the name of the data file is gse66351_1.rda.

resGSE1 <- resourcer::newResource(
  name = "GSE66351_1",
  url = "https://armadillo-demo.molgenis.net/storage/projects/omics/objects/ewas%2Fgse66351_1.rda",
  format = "ExpressionSet"
)
resGSE2 <- resourcer::newResource(
  name = "GSE66351_1",
  url = "https://armadillo-demo.molgenis.net/storage/projects/omics/objects/ewas%2Fgse66351_1.rda",
  format = "ExpressionSet"
)

armadillo.upload_resource(project="omics", folder="ewas", resource = resGSE1, name = "GSE66351_1")
#> Compressing...
#> Uploaded ewas/GSE66351_1
armadillo.upload_resource(project="omics", folder="ewas", resource = resGSE2, name = "GSE66351_2")
#> Compressing...
#> Uploaded ewas/GSE66351_2

The data is now available for researcher to assign.

MolgenisArmadillo documentation built on Nov. 17, 2023, 5:07 p.m.