create_features_df() and added an example gene-level
SCNA data frame example_gene_scna_tableorg.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.MCR_table. The coordinates were
converted to hg19 (from hg18)caret::predict.train explicitcreate_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”TCGA_MTL_fit and
specific_thresholds after fixing the issue abovena.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 = “.”)determine_hotspot_genes() to able to use
occurrence annotations from different versions of COSMICInitial release
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