Class: Mspire::Lipid::Search::Hit

Inherits:
Object
  • Object
show all
Defined in:
lib/mspire/lipid/search/hit.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(hash = {}) ⇒ Hit

Returns a new instance of Hit.



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# File 'lib/mspire/lipid/search/hit.rb', line 25

def initialize(hash={})
  hash.each {|k,v| instance_variable_set("@#{k}", v) }
end

Instance Attribute Details

#db_isobar_group ⇒ Object

the db_isobar_group this hit is associated with. Each hit is only associated with a single db_isobar_group!



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# File 'lib/mspire/lipid/search/hit.rb', line 8

def db_isobar_group
  @db_isobar_group
end

#decoy_qvalue ⇒ Object

qvalue derived from decoy testing



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# File 'lib/mspire/lipid/search/hit.rb', line 19

def decoy_qvalue
  @decoy_qvalue
end

#observed_mz ⇒ Object

the experimental m/z value



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# File 'lib/mspire/lipid/search/hit.rb', line 10

def observed_mz
  @observed_mz
end

#probability_distribution ⇒ Object

the probability distribution that can be used to determine its pvalue



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# File 'lib/mspire/lipid/search/hit.rb', line 23

def probability_distribution
  @probability_distribution
end

#pvalue ⇒ Object

the probability the hit is due to random chance



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# File 'lib/mspire/lipid/search/hit.rb', line 12

def pvalue
  @pvalue
end

#qvalue ⇒ Object

the FDR if the threshold accepts this pvalue. Note that this value is relative to the number of tests performed and not completely intrinsic to the hit itself.



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# File 'lib/mspire/lipid/search/hit.rb', line 16

def qvalue
  @qvalue
end

Instance Method Details

#delta ⇒ Object Also known as: amu

observed_mz - query m/z



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# File 'lib/mspire/lipid/search/hit.rb', line 30

def delta
  @observed_mz - @db_isobar_group.first.mz.to_f
end

#delta_abs ⇒ Object

the absolute value of distance from true val



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# File 'lib/mspire/lipid/search/hit.rb', line 37

def delta_abs
  delta.abs
end

#inspect ⇒ Object 



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# File 'lib/mspire/lipid/search/hit.rb', line 50

def inspect
  "<<#{super} -- <ppm=#{ppm} delta=#{delta} theoretical_mz=#{theoretical_mz}>>"
end

#ppm ⇒ Object

parts per million (divided by theoretical m/z)



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# File 'lib/mspire/lipid/search/hit.rb', line 42

def ppm
  (delta / @db_isobar_group.first.mz) * 1e6
end

#theoretical_mz ⇒ Object 



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# File 'lib/mspire/lipid/search/hit.rb', line 46

def theoretical_mz
  @db_isobar_group.first.mz
end