R/DominoEffect.R

In DominoEffect: Identification and Annotation of Protein Hotspot Residues

DominoEffect <- function(mutation_dataset, gene_data, snp_data,
min_n_muts = 5, MAF_thresh = 0.01,
flanking_region = c(200, 300),
poisson.thr = 0.01, percentage.thr = 0.15,
ratio.thr = 45, approach = "percentage", write_to_file = "NO"){

    results <- identify_hotspots(mutation_dataset, gene_data, snp_data,
                                 min_n_muts, MAF_thresh, flanking_region,
                                 poisson.thr, percentage.thr, ratio.thr, 
                                 approach)

    hotspot_mutations <- map_to_func_elem(results, write_to_file, 
                                          ens_release = "http://feb2014.archive.ensembl.org")
    message ("   ***FINISHED***")
    return(hotspot_mutations)
}