Method: Annotations::GO.get_genes_nth

Defined in:

lib/MARQ/annotations.rb

.get_genes_nth(dataset, num_genes) ⇒ Object

# File 'lib/MARQ/annotations.rb', line 438

def self.get_genes_nth(dataset, num_genes)
  path = MARQ.dataset_path(dataset)

  experiments = File.open(path + '.experiments').collect{|l| l.chomp.strip}
  genes       = File.open(path + '.codes').collect{|l| l.chomp.strip}
  total_genes = genes.length

  genes_up = {}
  genes_down = {}
  experiments.each{|exp| genes_up[exp] = []; genes_down[exp] = []}

  File.open(path + '.orders').each_with_index{|l, i|
    values = l.chomp.split(/\t/)
    experiments.zip(values).each{|p|
      name = p.first
      value = p.last
      next if p.last == "NA"
      genes_up[name]   <<  genes[i] if value.to_i < num_genes
      genes_down[name] <<  genes[i] if value.to_i > total_genes - num_genes
    }
  }

  {:up => genes_up, :down => genes_down}
end