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#
# = bio/db/kegg/expression.rb - KEGG EXPRESSION database class
#
# Copyright:: Copyright (C) 2001-2003, 2005
# Shuichi Kawashima <shuichi@hgc.jp>,
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id: expression.rb,v 1.11 2007/04/05 23:35:41 trevor Exp $
#
require "bio/db"
module Bio
class KEGG
class EXPRESSION
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
attr_reader :orf2val
attr_reader :orf2rgb
attr_reader :orf2ratio
attr_reader :max_intensity
def control_avg
sum = 0.0
@orf2val.values.each do |v|
sum += v[0] - v[1]
end
sum/orf2val.size
end
def target_avg
sum = 0.0
@orf2val.values.each do |v|
sum += v[2] - v[3]
end
sum/orf2val.size
end
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
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
def control_sd
var = self.control_var
Math.sqrt(var)
end
def target_sd
var = self.target_var
Math.sqrt(var)
end
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
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
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
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
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
end # class EXPRESSION
end # class KEGG
end # module Bio
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