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

.dpi(pi_rt, pi_v1v3) ⇒ Array

function for predict Days Post Infection

Returns:

  • (Array) —

    Array of [DPI, lwr, upr] for DPI prediction as [Numerics]



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# File 'lib/viral_seq/recency.rb', line 56

def self.dpi(pi_rt, pi_v1v3)

  if pi_rt.is_a? Numeric and pi_v1v3.is_a? Numeric
    pi = pi_rt*100 + pi_v1v3*100
    model_file = "rt_v1v3_fit.Rdata"
    var = "combined_perc"
  elsif pi_rt.is_a? Numeric
    pi = pi_rt*100
    model_file = "rt_only_fit.Rdata"
    var = "rtperc"
  elsif pi_v1v3.is_a? Numeric
    pi = pi_v1v3*100
    model_file = "v1v3_only_fit.Rdata"
    var = "v1v3perc"
  else
    return ["NA", "NA", "NA"]
  end
  path = File.join( ViralSeq.root, "viral_seq", "util", "recency_model", model_file)
  data_str = `Rscript -e 'fit = readRDS("#{path}"); test = data.frame(#{var} = #{pi}); pre= predict(fit, test, interval = "prediction", level = 0.9); cat(pre)'`
  dpi_array = data_str.split("\s")
  dpi = dpi_array[0].to_f.round(1)
  lwr = dpi_array[1].to_f.round(1)
  upr = dpi_array[2].to_f.round(1)
  if lwr < 0
    return [dpi, 0.0, upr]
  else
    return [dpi, lwr, upr]
  end
end

.possible_dual_infection(recency, dpi) ⇒ String

given ‘recency` and `dpi` predict if possible dual infection exists

Returns:

  • (String) —

    “Yes”, “No”, or “insufficient data”



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# File 'lib/viral_seq/recency.rb', line 91

def self.possible_dual_infection(recency, dpi)
  if ["recent", "chronic", "indeterminant"].include? recency and dpi[0].is_a? Numeric
    if recency == "indeterminant" and dpi[0] > 730
      "Yes"
    else
      "No"
    end
  else
    "insufficient data"
  end
end