class Bio::PAML::Codeml::PositiveSite
A record of codon sites, across the sequences in the alignment, showing evidence of positive selection.
This class is used for storing both codeml’s full Bayesian and naive Bayesian analysis
Attributes
aaref[R]
omega[R]
p[R]
position[R]
probability[R]
Public Class Methods
new(fields)
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# File lib/bio/appl/paml/codeml/report.rb 492 def initialize fields 493 @position = fields[0].to_i 494 @aaref = fields[1].to_s 495 @probability = fields[2].to_f 496 @omega = fields[3].to_f 497 end
Public Instance Methods
dN_dS()
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Return dN/dS (or omega) for this codon
# File lib/bio/appl/paml/codeml/report.rb 500 def dN_dS 501 omega 502 end
Also aliased as: w
to_a()
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Return contents as Array - useful for printing
# File lib/bio/appl/paml/codeml/report.rb 509 def to_a 510 [ @position, @aaref, @probability, @omega ] 511 end