NEWS

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pgxRpi 1.5.3 (2025-05-15)

• Added filter_pattern parameter to pgxLoader to enable keyword-based search of available filter terms.
• Improved warning messages to include HTTP status codes for failed requests, and clarified domain information in queries involving multiple domains.
• Simplified domain field description by retaining only the domain address.

pgxRpi 1.3.3 (2025-02-12)

• Updated the "sample_count" extraction method from "services/collations" to beacon count response, expanding counts to include all available entities (analyses, biosamples, individuals) and changing the type from "sample_count" to "counts" in pgxLoader.
• Enabled parallel queries across multiple resource domains (in pgxmetaLoader).
• Optimized code for Beacon response mapping and updated YAML mapping rules.

• Updated pgxfreqplot to set ylim as max(lowfreq, highfreq), ensuring proper scaling when high-level frequency exceeds low-level frequency.
• Replaced id parameter with the standard query path for Beacon queries.
• Modified variant data retrieval in seg format to fetch directly from the service API.

pgxRpi 1.3.1 (2025-01-14)

• Removed the pgxFilter function and incorporated its functionality into pgxLoader with the "filtering_terms" type, following the Beacon v2 response mapping.
• Updated vignette filenames for improved clarity.
• Made parameter checks more flexible for Beacon queries.

pgxRpi 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.

pgxRpi 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.

pgxRpi 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.

pgxRpi 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.

pgxRpi 1.1.3 (2024-06-14)

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

pgxRpi 1.1.2 (2024-05-03)

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

pgxRpi 0.99.7 (2023-10-20)

• Add pgxFilter function to expose all available filters.

pgxRpi 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.

pgxRpi 0.99.0 (2023-08-25)

• Submitted to Bioconductor