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

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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

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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 v0.2.0

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 v0.1.1

initial release