Class: MS::Lipid::Search::ProbabilityDistribution

Inherits:
Object
  • Object
show all
Defined in:
lib/ms/lipid/search/probability_distribution.rb

Constant Summary collapse

DEFAULT_TYPE = 
:ppm
R = 
Rserve::Simpler.new

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(location, scale, shape, type = DEFAULT_TYPE) ⇒ ProbabilityDistribution

Returns a new instance of ProbabilityDistribution.



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# File 'lib/ms/lipid/search/probability_distribution.rb', line 13

def initialize(location, scale, shape, type=DEFAULT_TYPE)
  @location, @scale, @shape = location, scale, shape
  @type = type
end

Instance Attribute Details

#location ⇒ Object

takes location, scale and shape parameters



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# File 'lib/ms/lipid/search/probability_distribution.rb', line 10

def location
  @location
end

#scale ⇒ Object

takes location, scale and shape parameters



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# File 'lib/ms/lipid/search/probability_distribution.rb', line 10

def scale
  @scale
end

#shape ⇒ Object

takes location, scale and shape parameters



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# File 'lib/ms/lipid/search/probability_distribution.rb', line 10

def shape
  @shape
end

#type ⇒ Object

type is :ppm or :delta_abs



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# File 'lib/ms/lipid/search/probability_distribution.rb', line 12

def type
  @type
end

Class Method Details

.deviations_to_probability_distribution(type, devs) ⇒ Object

returns an EVD object



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# File 'lib/ms/lipid/search/probability_distribution.rb', line 41

def self.deviations_to_probability_distribution(type, devs)
  %w(ismev evd).each {|lib| require_r_library(lib) }
  params = R.converse("m <- gev.fit(log(devs_r))\n c(m$mle[1], m$mle[2], m$mle[3])", :devs_r => devs )
  self.new(*params, type)
end

.require_r_library(lib) ⇒ Object 



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# File 'lib/ms/lipid/search/probability_distribution.rb', line 30

def self.require_r_library(lib)
  reply = R.converse "library(#{lib})"
  unless reply.size > 4  # ~roughly
    $stderr.puts "The libraries ismev and evd must be installed in your R env!"
    $stderr.puts "From within R (works best if R is started with sudo or root for installing):"
    $stderr.puts %Q{install.packages("ismev") ; install.packages("evd")}
    raise "must have R (rserve) and ismev and evd installed!"
  end
end

Instance Method Details

#pvalue(hit) ⇒ Object

takes a deviation and returns the pvalue



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# File 'lib/ms/lipid/search/probability_distribution.rb', line 19

def pvalue(hit)
  R.converse "pgev(log(#{hit.send(type)}), #{@location}, #{@scale}, #{@shape})"
end

#pvalues(hits) ⇒ Object

same as pvalue, just tries to limit the number of calls to R to speed things up!



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# File 'lib/ms/lipid/search/probability_distribution.rb', line 25

def pvalues(hits)
  deltas = hits.map {|v| v.send(type).abs }
  R.converse("sapply(r_devs, function(elt) pgev(log(elt), #{@location}, #{@scale}, #{@shape}))", :r_devs => deltas)
end