class Bio::KEGG::EXPRESSION

Attributes

max_intensity[R]
orf2ratio[R]
orf2rgb[R]
orf2val[R]

Public Class Methods

new(entry) click to toggle source
# File lib/bio/db/kegg/expression.rb, line 19
def initialize(entry)
  @orf2val   = Hash.new('')
  @orf2rgb   = Hash.new('')
  @orf2ratio = Hash.new('')
  @max_intensity = 10000
  entry.split("\n").each do |line|
    unless /^#/ =~ line
      ary = line.split("\t")
      orf = ary.shift
      val = ary[2, 4].collect {|x| x.to_f}
      @orf2val[orf] = val 
    end
  end
end

Public Instance Methods

control_avg() click to toggle source
# File lib/bio/db/kegg/expression.rb, line 38
def control_avg
  sum = 0.0
  @orf2val.values.each do |v|
    sum += v[0] - v[1]
  end
  sum/orf2val.size
end
control_sd() click to toggle source
# File lib/bio/db/kegg/expression.rb, line 74
def control_sd
  var = self.control_var
  Math.sqrt(var)
end
control_var() click to toggle source
# File lib/bio/db/kegg/expression.rb, line 54
def control_var
  sum = 0.0
  avg = self.control_avg
  @orf2val.values.each do |v|
    tmp = v[0] - v[1]
    sum += (tmp - avg)*(tmp - avg)
  end
  sum/orf2val.size
end
down_regulated(num=20, threshold=nil) click to toggle source
# File lib/bio/db/kegg/expression.rb, line 98
def down_regulated(num=20, threshold=nil)
  logy_minus_logx
  ary = @orf2ratio.to_a.sort{|a, b| a[1] <=> b[1]}
  if threshold != nil
    i = 0
    while ary[i][1] < threshold
      i += 1
    end
    return ary[0..i]
  else
    return ary[0..num-1]
  end
end
logy_minus_logx() click to toggle source
# File lib/bio/db/kegg/expression.rb, line 126
def logy_minus_logx
  @orf2val.each do |k, v|
    @orf2ratio[k] = (1.0/Math.log10(2))*(Math.log10(v[2]-v[3]) - Math.log10(v[0]-v[1]))
  end
end
regulated(num=20, threshold=nil) click to toggle source
# File lib/bio/db/kegg/expression.rb, line 112
def regulated(num=20, threshold=nil)
  logy_minus_logx
  ary = @orf2ratio.to_a.sort{|a, b| b[1].abs <=> a[1].abs}
  if threshold != nil
    i = 0
    while ary[i][1].abs > threshold
      i += 1
    end
    return ary[0..i]
  else
    return ary[0..num-1]
  end
end
target_avg() click to toggle source
# File lib/bio/db/kegg/expression.rb, line 46
def target_avg
  sum = 0.0
  @orf2val.values.each do |v|
    sum += v[2] - v[3]
  end
  sum/orf2val.size
end
target_sd() click to toggle source
# File lib/bio/db/kegg/expression.rb, line 79
def target_sd
  var = self.target_var
  Math.sqrt(var)
end
target_var() click to toggle source
# File lib/bio/db/kegg/expression.rb, line 64
def target_var
  sum = 0.0
  avg = self.target_avg
  @orf2val.values.each do |v|
    tmp = v[2] - v[3]
    sum += (tmp - avg)*(tmp - avg)
  end
  sum/orf2val.size
end
up_regulated(num=20, threshold=nil) click to toggle source
# File lib/bio/db/kegg/expression.rb, line 84
def up_regulated(num=20, threshold=nil)
  logy_minus_logx
  ary = @orf2ratio.to_a.sort{|a, b| b[1] <=> a[1]}
  if threshold != nil
    i = 0
    while ary[i][1] > threshold
      i += 1
    end
    return ary[0..i]
  else
    return ary[0..num-1]
  end
end
val2rgb() click to toggle source
# File lib/bio/db/kegg/expression.rb, line 132
def val2rgb
  col_unit = @max_intensity/255
  @orf2val.each do |k, v|
    tmp_val = ((v[0] - v[1])/col_unit).to_i
    if tmp_val > 255
      g = "ff" 
    else
      g = format("%02x", tmp_val)
    end
    tmp_val = ((v[2] - v[3])/col_unit).to_i
    if tmp_val > 255
      r = "ff" 
    else
      r = format("%02x", tmp_val)
    end
    @orf2rgb[k] = r + g + "00"
  end

end