Changelog

Source: NEWS.md

driveR (development version)

driveR 0.5.0

Major Changes

• added support for gene-level SCNA data frames to be used as input for create_features_df() and added an example gene-level SCNA data frame example_gene_scna_table

Minor changes and bug fixes

• Moved org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene and TxDb.Hsapiens.UCSC.hg38.knownGene from “Imports” to “Suggests” per new CRAN policy. Relevant functions raise error if the required package is not installed.

driveR 0.4.12023-08-19

Minor changes and bug fixes

• fixed a CRAN error due to a package documentation issue (#7)

driveR 0.4.02022-08-15

Major Changes

• Added GRCh38 support

driveR 0.3.02022-01-18

Major Changes

• Updated the cancer-type-specific thresholds

Minor changes and bug fixes

• Updated citation to the method’s article where necessary

driveR 0.2.12020-11-25

Major Changes

• Updated the MTL model after fixing the issue below
• Fixed issue in MCR_table. The coordinates were converted to hg19 (from hg18)

Minor changes and bug fixes

• Made use of caret::predict.train explicit
• Removed ‘Homo.sapiens’ from Imports field (not used)

driveR 0.2.02020-11-19

Major Changes

• Fixed an issue in create_SCNA_score_df() where the SCNA score was not calculated because the column name for “MCR_overlap_percent” was incorrectly assigned as “transcript_overlap_percent”
• Updated the MTL classification model TCGA_MTL_fit and specific_thresholds after fixing the issue above

Minor changes and bug fixes

• Updated citation information, correcting author name
• Minor changes in utility functions
• Added the na.string argument to create_noncoding_impact_score_df(), predict_coding_impact() and create_features_df() as the string that was used to indicate when a score is not available during annotation with ANNOVAR (default = “.”)
• Generalized determine_hotspot_genes() to able to use occurrence annotations from different versions of COSMIC
• Updated all data

driver 0.1.12020-11-18

Initial release