Class: Bioinform::PCM

Inherits:
PM show all
Defined in:
lib/bioinform/data_models/pcm.rb

Instance Attribute Summary

Attributes inherited from PM

#matrix, #parameters

Instance Method Summary collapse

Methods inherited from PM

#==, #as_pcm, #as_ppm, #as_pwm, choose_parser, #discrete, #discrete!, #dup, #each_position, #initialize, #left_augment, #left_augment!, #length, #pretty_string, #probability, #reverse_complement, #reverse_complement!, #right_augment, #right_augment!, split_on_motifs, #to_hash, #to_s, #valid?, valid_matrix?, #vocabulary_volume, zero_column

Methods included from Parameters

#get_parameters, included, #parameter_defined?, #parameters, #set_parameters

Constructor Details

This class inherits a constructor from Bioinform::PM

Instance Method Details

#count ⇒ Object 



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# File 'lib/bioinform/data_models/pcm.rb', line 8

def count
  matrix.first.inject(&:+)
end

#to_pcm ⇒ Object 



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# File 'lib/bioinform/data_models/pcm.rb', line 12

def to_pcm
  self
end

#to_ppm ⇒ Object 



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# File 'lib/bioinform/data_models/pcm.rb', line 20

def to_ppm
  ConversionAlgorithms::PCM2PPMConverter.convert(self)
end

#to_pwm(pseudocount = Math.log(count)) ⇒ Object 



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# File 'lib/bioinform/data_models/pcm.rb', line 16

def to_pwm(pseudocount = Math.log(count))
  ConversionAlgorithms::PCM2PWMConverter.convert(self, pseudocount: pseudocount)
end