Module: OrderedList

Defined in:
lib/rbbt/statistics/random_walk.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#total_weights ⇒ Object

Returns the value of attribute total_weights.



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# File 'lib/rbbt/statistics/random_walk.rb', line 338

def total_weights
  @total_weights
end

#weights ⇒ Object

Returns the value of attribute weights.



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# File 'lib/rbbt/statistics/random_walk.rb', line 338

def weights
  @weights
end

Class Method Details

.draw_hits(list, set, filename = nil, options = {}) ⇒ Object 



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# File 'lib/rbbt/statistics/random_walk.rb', line 360

def self.draw_hits(list, set, filename = nil, options = {})
  hits = OrderedList.hits(list, set)
  RandomWalk.draw_hits(hits, list.length, filename, options)
end

.hits(list, set) ⇒ Object 



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# File 'lib/rbbt/statistics/random_walk.rb', line 351

def self.hits(list, set)
  set = Set.new(set) unless Set === set
  hits = []
  list.each_with_index do |e,i|
    hits << i + 1 if set.include? e # count from 1
  end
  hits
end

.setup(list, weights = nil, total_weights = nil) ⇒ Object 



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# File 'lib/rbbt/statistics/random_walk.rb', line 340

def self.setup(list, weights = nil, total_weights = nil)
  list.extend OrderedList
  list.weights = weights
  if weights and total_weights.nil?
    list.total_weights = Misc.sum(weights)
  else
    list.total_weights = total_weights
  end
  list
end

Instance Method Details

#draw_hits(set, filename = nil, options = {}) ⇒ Object 



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# File 'lib/rbbt/statistics/random_walk.rb', line 382

def draw_hits(set, filename = nil, options = {})
  OrderedList.draw_hits(self, set, filename, options)
end

#hits(set) ⇒ Object 



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# File 'lib/rbbt/statistics/random_walk.rb', line 365

def hits(set)
  OrderedList.hits(self, set)
end

#pvalue(set, cutoff = 0.1, options = {}) ⇒ Object

def pvalue(set, options = {})

set = Set.new(set.compact) unless Set === set
options = Misc.add_defaults options, :permutations => 10000, :missing => 0
hits = hits(set)
score = RandomWalk.score(hits.sort, self.length, 0)
permutations = RandomWalk.permutations(set.length, self.length, options[:missing], options[:permutations])
RandomWalk.pvalue(permutations, score)

end



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# File 'lib/rbbt/statistics/random_walk.rb', line 395

def pvalue(set, cutoff = 0.1, options = {})
  set = Set.new(set.compact) unless Set === set
  options = Misc.add_defaults options, :permutations => 10000, :missing => 0
  permutations, missing, persist_permutations = Misc.process_options options, :permutations, :missing, :persist_permutations

  hits = hits(set)
 
  return 1.0 if hits.empty?

  target_score = RandomWalk.score(hits.sort, self.length, missing)

  if persist_permutations
    permutations = RandomWalk.persisted_permutations(set.length, self.length, missing, permutations)
    RandomWalk.pvalue(permutations, target_score)
  else
    # P-value computation
    target_score_abs = target_score.abs

    max = (permutations.to_f * cutoff).ceil

    size = set.length
    total = self.length
    better_permutation_score_count = 1
    if size == 0
      1.0
    else
      (1..permutations).each do
        p= []
        RandomWalk.sample_without_replacement(total, size, p)

        permutation_score = RandomWalk.score(p.sort, total, missing).abs
        if permutation_score.abs > target_score_abs
          better_permutation_score_count += 1
        end

        return 1.0 if better_permutation_score_count > max
      end
      p = (better_permutation_score_count.to_f + 1) / permutations
      p = -p if target_score < 0
      p
    end
  end
end

#pvalue_weights(set, cutoff = 0.1, options = {}) ⇒ Object 



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# File 'lib/rbbt/statistics/random_walk.rb', line 439

def pvalue_weights(set, cutoff = 0.1, options = {})
  raise "No weight defined" if @weights.nil?
  @total_weights ||= Misc.sum(@weights)

  set = Set.new(set.compact) unless Set === set
  options = Misc.add_defaults options, :permutations => 10000, :missing => 0
  permutations, missing = Misc.process_options options, :permutations, :missing

  hits = hits(set)

  return 1.0 if hits.empty?

  target_score = RandomWalk.score_weights(hits.sort, @weights, @total_weights, self.length, 0)
  target_score_abs = target_score.abs

  max = (permutations.to_f * cutoff).ceil

  size = set.length
  total = self.length
  better_permutation_score_count = 1
  if size == 0
    1.0
  else
    (1..permutations).each do
      p= []
      RandomWalk.sample_without_replacement(total, size, p)

      permutation_score = RandomWalk.score_weights(p.sort, @weights, @total_weights, total, missing).abs
      if permutation_score.abs > target_score_abs
        better_permutation_score_count += 1
      end

      return 1.0 if better_permutation_score_count > max
    end
    p = (better_permutation_score_count.to_f + 1) / permutations
    p = -p if target_score < 0
    p
  end
end

#score(set) ⇒ Object 



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# File 'lib/rbbt/statistics/random_walk.rb', line 369

def score(set)
  hits = hits(set)
  RandomWalk.score(hits.sort, self.length, 0)
end

#score_weights(set) ⇒ Object 



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# File 'lib/rbbt/statistics/random_walk.rb', line 374

def score_weights(set)
  raise "No weight defined" if @weights.nil?
  @total_weights ||= Misc.sum(@weights)
  hits = hits(set)
  RandomWalk.score_weights(hits.sort, @weights, @total_weights, self.length, 0)
end