Module: ViralSeq::Recency

Defined in:
lib/viral_seq/recency.rb

Overview

recency prediction function based on HIV MPID-NGS

See Also:

Class Method Summary collapse

Class Method Details

.define(tcs_RT: nil, tcs_V1V3: nil, pi_RT: nil, dist20_RT: nil, pi_V1V3: nil, dist20_V1V3: nil) ⇒ String

Returns determination of the recency.

Returns:

  • (String) —

    determination of the recency



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# File 'lib/viral_seq/recency.rb', line 16

def self.define(tcs_RT: nil,
                 tcs_V1V3: nil,
                 pi_RT: nil,
                 dist20_RT: nil,
                 pi_V1V3: nil,
                 dist20_V1V3: nil)
  tcs_RT ||= 0
  tcs_V1V3 ||= 0
  if (tcs_RT >= 3 && pi_RT) and (tcs_V1V3 >= 3 && pi_V1V3)
    if (pi_RT + pi_V1V3) < 0.0103
        recency = "recent"
    elsif (pi_RT + pi_V1V3) >= 0.0103 and (dist20_RT + dist20_V1V3) >= 0.006
        recency = "chronic"
    else
        recency = "indeterminant"
    end
  elsif (tcs_RT >= 3 && pi_RT) and tcs_V1V3 < 3
    if pi_RT < 0.0021
      recency = "recent"
    elsif pi_RT >= 0.0021 and dist20_RT >= 0.001
      recency = "chronic"
    else
      recency = "indeterminant"
    end
  elsif (tcs_V1V3 >= 3 && pi_V1V3)
    if pi_V1V3 >= 0.0103 and dist20_V1V3 >= 0.006
      recency = "chronic"
    else
      recency = "insufficient data"
    end
  else
    recency = "insufficient data"
  end
  return recency
end