module BioVcf::Variant

Public Class Methods

apply_threshold(t,normal,tumor) click to toggle source
# File lib/bio-vcf/variant.rb, line 31
def Variant.apply_threshold t,normal,tumor
  normal2 = normal.map{|v| (v>t ? 0 : v) }
  tumor2 = tumor.each_with_index.map{|v,i| (normal2[i]==0 ? 0 : v) }
  return normal2,tumor2
end
diff(normal,tumor) click to toggle source
# File lib/bio-vcf/variant.rb, line 5
def Variant.diff normal,tumor
  tumor.each_with_index.map {|t,i| t-normal[i]}
end
index(normal,tumor) click to toggle source
# File lib/bio-vcf/variant.rb, line 25
def Variant.index normal,tumor
  rd = relative_diff(normal,tumor) 
  max = rd.reduce(0){|mem,v| (v>mem ? v : mem) }
  rd.index(max)
end
relative_diff(normal,tumor) click to toggle source
# File lib/bio-vcf/variant.rb, line 14
def Variant.relative_diff normal,tumor
  d = diff(normal,tumor)
  total = tumor.each_with_index.map {|t,i| t+normal[i]}
  total.each_with_index.map {|t,i| (t==0 ? 0 : ((d[i].to_f/t)*100.0).round/100.0)}
end
relative_threshold_diff(t,normal,tumor) click to toggle source
# File lib/bio-vcf/variant.rb, line 20
def Variant.relative_threshold_diff t,normal,tumor
  normal2,tumor2 = apply_threshold(t,normal,tumor)
  relative_diff(normal2,tumor2)
end
threshold_diff(t,normal,tumor) click to toggle source
# File lib/bio-vcf/variant.rb, line 9
def Variant.threshold_diff t,normal,tumor
  normal2,tumor2 = apply_threshold(t,normal,tumor)
  diff(normal2,tumor2)
end