Module: BioVcf::Variant

Defined in:
lib/bio-vcf/variant.rb

Class Method Summary collapse

Class Method Details

.apply_threshold(t, normal, tumor) ⇒ Object 



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# 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) ⇒ Object 



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# 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) ⇒ Object 



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# 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) ⇒ Object 



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# 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) ⇒ Object 



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# 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) ⇒ Object 



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# 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