Class: Cheripic::Bfr

Inherits:
Object
  • Object
show all
Defined in:
lib/cheripic/bfr.rb

Overview

A class to calculate bulk frequency ratio (bfr) using one or two hashes of base fractions resulted from pileup

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Attribute Details

#bfr_adj ⇒ Float

Returns a float value to adjust the bfr calculation.

Returns:

  • (Float) —

    a float value to adjust the bfr calculation



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# File 'lib/cheripic/bfr.rb', line 12

class Bfr

  attr_accessor :bfr_adj

  # A method to get bulk frequency ratio (bfr) for selected hemi snps.
  #   This is done by selecting which hash (mutant or background) to use for bfr calculation
  #   either calculates fraction or bfr
  #   and ignores positions with complex variants.
  # @param mut_hash [Hash] a hash of base fractions from pileup of mutant bulk
  # @param bg_hash [Hash] a hash of base fractions from pileup of background bulk
  # @return [Float] a ratio calculated
  def self.get_bfr(mut_hash, bg_hash='')
    @bfr_adj = Options.bfr_adjust
    if bg_hash != ''
      # checking if only two vars in base hash and that includes ref
      # checking if only one var in hemi snp
      # suggests enrichment for one of two alleles
      if mut_hash.length == 2 and mut_hash.key?(:ref)
        bfr = calculate_bfr(mut_hash, bg_hash)
      elsif bg_hash.length == 2  and bg_hash.key?(:ref)
        bfr = calculate_bfr(bg_hash, mut_hash)
      elsif mut_hash.length == 1 and mut_hash[:ref] == nil
        bfr = calculate_bfr(mut_hash, bg_hash)
      elsif bg_hash.length == 1 and bg_hash[:ref] == nil
        bfr = calculate_bfr(bg_hash, mut_hash)
      else # complex
        bfr = ''
      end
    elsif mut_hash.length == 2 and mut_hash.key?(:ref)
      bfr = calc_fraction(mut_hash)[0]/ @bfr_adj
    elsif mut_hash.length == 1 and mut_hash[:ref] == nil
      bfr = calc_fraction(mut_hash)[0]/ @bfr_adj
    else
      bfr = ''
    end
    bfr
  end

  # A method to calculate bfr using a base fraction hash with hemi-snp
  # @param two_key_hash [Hash] a hash of base fractions from pileup with 2 keys (a ref and variant base)
  # @param other_hash [Hash] a hash of base fractions from pileup
  # @return [Float] a ratio calculated
  def self.calculate_bfr(two_key_hash, other_hash)
    # if :ref is absent such as below noise depth, then set to zero
    unless two_key_hash.key?(:ref)
      two_key_hash[:ref] = 0
    end
    unless other_hash.key?(:ref)
      other_hash[:ref] = 0
    end
    frac_1, base = calc_fraction(two_key_hash)
    if other_hash.key?(base)
      sum = other_hash[base] + other_hash[:ref] + @bfr_adj
      frac_2 = (other_hash[base] + @bfr_adj)/sum
    else
      sum = other_hash[:ref] + @bfr_adj
      frac_2 = @bfr_adj/sum
    end
    # making sure ratio is always 1 or grater
    if frac_1 > frac_2
      bfr = frac_1/frac_2
    else
      bfr = frac_2/frac_1
    end
    bfr
  end

  # A method to calculate ratio using a base fraction hash
  # @param hash [Hash] a hash of base fractions from pileup with 2 or 1 keys
  # @return [Array<Float><String>] an array of ratio calculated and base character
  def self.calc_fraction(hash)
    unless hash.key?(:ref)
      hash[:ref] = 0
    end
    array = hash.keys
    sum = hash[array[0]] + hash[array[1]] + @bfr_adj
    if array[0] == :ref
      frac = (hash[array[1]] + @bfr_adj)/sum
      base = array[1]
    else
      frac = (hash[array[0]] + @bfr_adj)/sum
      base = array[0]
    end
    [frac, base]
  end

end

Class Method Details

.calc_fraction(hash) ⇒ Array<Float><String>

A method to calculate ratio using a base fraction hash

Parameters:

  • hash (Hash) —

    a hash of base fractions from pileup with 2 or 1 keys

Returns:

  • (Array<Float><String>) —

    an array of ratio calculated and base character



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# File 'lib/cheripic/bfr.rb', line 82

def self.calc_fraction(hash)
  unless hash.key?(:ref)
    hash[:ref] = 0
  end
  array = hash.keys
  sum = hash[array[0]] + hash[array[1]] + @bfr_adj
  if array[0] == :ref
    frac = (hash[array[1]] + @bfr_adj)/sum
    base = array[1]
  else
    frac = (hash[array[0]] + @bfr_adj)/sum
    base = array[0]
  end
  [frac, base]
end

.calculate_bfr(two_key_hash, other_hash) ⇒ Float

A method to calculate bfr using a base fraction hash with hemi-snp

Parameters:

  • two_key_hash (Hash) —

    a hash of base fractions from pileup with 2 keys (a ref and variant base)

  • other_hash (Hash) —

    a hash of base fractions from pileup

Returns:

  • (Float) —

    a ratio calculated



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# File 'lib/cheripic/bfr.rb', line 54

def self.calculate_bfr(two_key_hash, other_hash)
  # if :ref is absent such as below noise depth, then set to zero
  unless two_key_hash.key?(:ref)
    two_key_hash[:ref] = 0
  end
  unless other_hash.key?(:ref)
    other_hash[:ref] = 0
  end
  frac_1, base = calc_fraction(two_key_hash)
  if other_hash.key?(base)
    sum = other_hash[base] + other_hash[:ref] + @bfr_adj
    frac_2 = (other_hash[base] + @bfr_adj)/sum
  else
    sum = other_hash[:ref] + @bfr_adj
    frac_2 = @bfr_adj/sum
  end
  # making sure ratio is always 1 or grater
  if frac_1 > frac_2
    bfr = frac_1/frac_2
  else
    bfr = frac_2/frac_1
  end
  bfr
end

.get_bfr(mut_hash, bg_hash = '') ⇒ Float

A method to get bulk frequency ratio (bfr) for selected hemi snps.

This is done by selecting which hash (mutant or background) to use for bfr calculation
either calculates fraction or bfr
and ignores positions with complex variants.

Parameters:

  • mut_hash (Hash) —

    a hash of base fractions from pileup of mutant bulk

  • bg_hash (Hash) (defaults to: '') —

    a hash of base fractions from pileup of background bulk

Returns:

  • (Float) —

    a ratio calculated



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# File 'lib/cheripic/bfr.rb', line 23

def self.get_bfr(mut_hash, bg_hash='')
  @bfr_adj = Options.bfr_adjust
  if bg_hash != ''
    # checking if only two vars in base hash and that includes ref
    # checking if only one var in hemi snp
    # suggests enrichment for one of two alleles
    if mut_hash.length == 2 and mut_hash.key?(:ref)
      bfr = calculate_bfr(mut_hash, bg_hash)
    elsif bg_hash.length == 2  and bg_hash.key?(:ref)
      bfr = calculate_bfr(bg_hash, mut_hash)
    elsif mut_hash.length == 1 and mut_hash[:ref] == nil
      bfr = calculate_bfr(mut_hash, bg_hash)
    elsif bg_hash.length == 1 and bg_hash[:ref] == nil
      bfr = calculate_bfr(bg_hash, mut_hash)
    else # complex
      bfr = ''
    end
  elsif mut_hash.length == 2 and mut_hash.key?(:ref)
    bfr = calc_fraction(mut_hash)[0]/ @bfr_adj
  elsif mut_hash.length == 1 and mut_hash[:ref] == nil
    bfr = calc_fraction(mut_hash)[0]/ @bfr_adj
  else
    bfr = ''
  end
  bfr
end