eucanconnect/datashield-R.Rmd at main · epigeny/eucanconnect · GitHub

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---
title: "DataSHIELD Python/R Notebook"
output: html_notebook
---

1. Establish connections with DataSHIELD nodes

```{r}
library(DSOpal)
library(dsBaseClient)
builder <- DSI::newDSLoginBuilder()
builder$append(server = "study1",  url = "https://opal-demo.obiba.org",
               user = "dsuser", password = "P@ssw0rd",
               profile = "default")
builder$append(server = "study2",  url = "https://opal-demo.obiba.org",
               user = "dsuser", password = "P@ssw0rd",
               profile = "default")
logindata <- builder$build()
options(datashield.progress = FALSE)
conns <- DSI::datashield.login(logins = logindata)
```

2. Utility functions

List profiles:

```{r}
datashield.profiles(conns)
```

List packages:

```{r}
datashield.pkg_status(conns)
```

List allowed methods:

```{r}
datashield.method_status(conns, type = "aggregate")
```

3. Make analysis

```{r}
datashield.assign.table(conns, "df", list(
  study1 = "CNSIM.CNSIM1",
  study2 = "CNSIM.CNSIM2"))
```

```{r}
ds.colnames('df')
```

```{r}
ds.mean('df$LAB_GLUC_ADJUSTED')
```

```{r}
ds.heatmapPlot('df$LAB_TSC', 'df$LAB_HDL', type = 'split')
```


```{r}
ds.histogram('df$LAB_GLUC_ADJUSTED', type = 'split')
```

4. Clean up


```{r}
datashield.logout(conns)
```