@@ -1,7 +1,7 @@

 Package: DominoEffect

 Type: Package

 Title: Identification and Annotation of Protein Hotspot Residues

-Version: 1.23.0

+Version: 1.23.1

 Author: Marija Buljan and Peter Blattmann

 Maintainer: Marija Buljan <[email protected]>, 

     Peter Blattmann <[email protected]>

@@ -1,16 +1,17 @@

 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)

+                         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",

+                         ens_release = "https://feb2014.archive.ensembl.org"){

+  

+  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 = ens_release)

+  message ("   ***FINISHED***")

+  return(hotspot_mutations)

 }