Prioritize Cancer Driver Genes

prioritize_driver_genes(features_df, cancer_type)

Arguments

features_df

the features data frame for all genes, containing the following columns:

gene_symbol: HGNC gene symbol
metaprediction_score: the maximum metapredictor (coding) impact score for the gene
noncoding_score: the maximum non-coding PHRED-scaled CADD score for the gene
scna_score: SCNA proxy score. SCNA density (SCNA/Mb) of the minimal common region (MCR) in which the gene is located
hotspot_double_hit: boolean indicating whether the gene is a hotspot gene (indication of oncogenes) or subject to double-hit (indication of tumor-suppressor genes)
phenolyzer_score: 'phenolyzer' score for the gene
hsa03320: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04010: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04020: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04024: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04060: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04066: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04110: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04115: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04150: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04151: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04210: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04310: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04330: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04340: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04350: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04370: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04510: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04512: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04520: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04630: boolean indicating whether or not the gene takes part in this KEGG pathway
hsa04915: boolean indicating whether or not the gene takes part in this KEGG pathway

cancer_type

short name of the cancer type. All available cancer types are listed in MTL_submodel_descriptions

Value

data frame with 3 columns:

gene_symbol: HGNC gene symbol
driverness_prob: estimated probability for each gene in features_df of being a cancer driver. The probabilities are calculated using the selected (via cancer_type) cancer type's sub-model.
prediction: prediction based on the cancer-type-specific threshold (either 'driver' or 'non-driver')

Examples

drivers_df <- prioritize_driver_genes(example_features_table, 'LUAD')

Prioritize Cancer Driver Genes

Arguments

Value

See also

Examples