# 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 via the Beacon v2 API with some extensions (BeaconPlus). 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 details on accessing biosample or individual information, get started from the vignette [Introduction_1_load_metadata](https://bioconductor.org/packages/devel/bioc/vignettes/pgxRpi/inst/doc/Introduction_1_load_metadata.html). To access CNV variant data, get started from this vignette [Introduction_2_query_variants](https://bioconductor.org/packages/devel/bioc/vignettes/pgxRpi/inst/doc/Introduction_2_query_variants.html). To access CNV frequency data, get started from this vignette [Introduction_3_access_cnv_frequency](https://bioconductor.org/packages/devel/bioc/vignettes/pgxRpi/inst/doc/Introduction_3_access_cnv_frequency.html). For processing local ".pgxseg" files, get started from this vignette [Introduction_4_process_pgxseg](https://bioconductor.org/packages/devel/bioc/vignettes/pgxRpi/inst/doc/Introduction_4_process_pgxseg.html). If you encounter problems, try to reinstall the latest version. If reinstallation doesn't help, please contact us.