Class: Bioinform::MotifModel::PCM

Inherits:
Object
  • Object
show all
Defined in:
lib/sequence_logo/ppm_support.rb

Instance Method Summary collapse

Instance Method Details

#get_logo(icd_mode) ⇒ Object 



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# File 'lib/sequence_logo/ppm_support.rb', line 54

def (icd_mode)
  case icd_mode.to_s
  when 'weblogo'
    
  when 'discrete'
    get_logo_discrete
  end
end

#get_logo_discrete ⇒ Object 



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# File 'lib/sequence_logo/ppm_support.rb', line 73

def get_logo_discrete
  each_position.map{|position|
    word_count = position.inject(0.0, &:+)
    icd4of4 = icd4of4(word_count)
    inf_content = (icd4of4 == 0) ? 1.0 : scale(position_infocod(position), relative_to: icd4of4)
    position.map{|el| (el / word_count) * inf_content }
  }
end

#get_logo_weblogo ⇒ Object 



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# File 'lib/sequence_logo/ppm_support.rb', line 63

def 
  each_position.map{|position|
    word_count = position.inject(0.0, &:+)
    inf_content = position.map{|el|
      (el == 0) ? 0 : (el / word_count) * Math.log2(el / word_count)
    }.inject(0.0, :+) + 2
    position.map{|el| (el / word_count) * inf_content / 2 }
  }
end