Class Bio::PAML::Codeml::PositiveSite
In: lib/bio/appl/paml/codeml/report.rb
Parent: Object

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

Methods

dN_dS   new   to_a   w  

External Aliases

probability -> p

Attributes

aaref  [R] 
omega  [R] 
position  [R] 
probability  [R] 

Public Class methods

[Source]

     # File lib/bio/appl/paml/codeml/report.rb, line 492
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

Return dN/dS (or omega) for this codon

[Source]

     # File lib/bio/appl/paml/codeml/report.rb, line 500
500:       def dN_dS
501:         omega
502:       end

Return contents as Array - useful for printing

[Source]

     # File lib/bio/appl/paml/codeml/report.rb, line 509
509:       def to_a
510:         [ @position, @aaref, @probability, @omega ]
511:       end
w()

Alias for dN_dS

[Validate]