pgxRpi

Welcome to our R wrapper package for Progenetix REST API that leverages the capabilities of Beacon v2 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 database via the Beacon v2 API with some extensions (BeaconPlus).

You can install this package using either of the following methods:

From Bioconductor

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("pgxRpi")

From Github for the latest development version

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.

To access CNV variant data, get started from this vignette Introduction_2_query_variants.

To access CNV frequency data, get started from this vignette Introduction_3_access_cnv_frequency.

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.