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NEWS.md

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Version: 0.99.0 (2023-08-25)

  • Submitted to Bioconductor

Version: 0.99.5 (2023-10-10)

  • Updated data structure for frequency data, transitioning from a simple list to Bioconductor containers.
  • Removed sections on survival analysis and frequency clustering analysis from the vignettes to align with the package's scope.

Version: 0.99.7 (2023-10-20)

  • Add pgxFilter function to expose all available filters.

Version: 1.1.2 (2024-05-03)

  • Add segtoFreq function to allow CNV frequency calculation from given segment data

Version: 1.1.3 (2024-06-14)

  • Add pgxMetaplot function to generate survival plots from metadata
  • Add num_cores parameter for parallel query of variants

Version: 1.1.5 (2024-07-30)

  • Added config/datatable_mappings.yaml to define mapping rules between Beacon JSON responses and data tables.
  • Modified metadata access to retrieve data directly from the Beacon API instead of using the services/sampletable API.
  • Enabled querying of analyses information.
  • Updated the type parameter in pgxLoader to align more closely with Beacon v2 model entities: biosamples, individuals, analyses, and g_variants.
  • Added entry_point parameter to pgxLoader.
  • Removed filterLogic parameter from pgxLoader.
  • Optimized parallel query for variants.
  • Cleaned up code and vignettes.

Version: 1.1.6 (2024-08-05)

  • Modified extract_general_results function to ensure it adapts correctly to arrays.
  • Moved callset and cnvstats data from the "g_variant" type to "cnv_fraction" to better align with data types.
  • Removed the pgxCount function and integrated its functionality into pgxLoader with the "sample_count" type, streamlining such query.

Version: 1.1.7 (2024-09-11)

  • Adapted to Progenetix API change: updated endpoint from "analyses/?output=cnvstats" to "services/cnvstats/".
  • The dataset parameter in pgxLoader is now used to select datasets directly from the Beacon response, rather than being used internally.
  • Modified pgxSegprocess to support usage with downloaded "pgxseg" files from Progenetix.

Version: 1.1.8 (2024-10-11)

  • Added support for accessing and visualizing level-specific CNV frequency data.
  • Enabled calculation of level-specific CNV frequencies from segment data.