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 0.4.1

Minor changes and bug fixes

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

driveR 0.4.0

Major Changes

• Added GRCh38 support

driveR 0.3.0

Major Changes

• Updated the cancer-type-specific thresholds

Minor changes and bug fixes

• Updated citation to the method's article where necessary

driveR 0.2.1

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 0.2.0

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 0.1.1

Initial release