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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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.