example_features_table {driveR}R Documentation

Example Features Table for Driver Prioritization

Description

The example dataset containing features for prioritizing cancer driver genes for the lung adenocarcinoma patient studied in Imielinski M, Greulich H, Kaplan B, et al. Oncogenic and sorafenib-sensitive ARAF mutations in lung adenocarcinoma. J Clin Invest. 2014;124(4):1582-6.

Usage

example_features_table

Format

A data frame with 4901 rows and 27 variables:

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

See Also

KEGG_cancer_pathways_descriptions for descriptions of KEGG "Pathways in cancer"-related pathways.


[Package driveR version 0.4.1 Index]