NEWS
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