# pgxRpi
Welcome to our R wrapper package for Progenetix REST API that leverages the capabilities of [Beacon v2](https://docs.genomebeacons.org/) specification. Please note that a stable internet connection is required for the query functionality. This package is aimed to simplify the process of accessing oncogenomic data from [Progenetix](https://progenetix.org/) database.
You can install this package using either of the following methods:
### From Bioconductor
```r
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pgxRpi")
```
### From Github for the latest development version
```r
if (!require("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("progenetix/pgxRpi")
```
For accessing metadata of biosamples/individuals, or learning more about filters, get started from the vignette Introduction_1_loadmetadata.
For accessing CNV variant data, get started from this vignette Introduction_2_loadvariants.
For accessing CNV frequency data, get started from this vignette Introduction_3_loadfrequency.
For processing local pgxseg files, get started from this vignette Introduction_4_process_pgxseg.
If you encounter problems, try to reinstall the latest version. If reinstallation doesn't help, please contact us.