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Kynurenine/Tryptophan ratio

Source: vignettes/articles/kyn_trp_ratio.Rmd
kyn_trp_ratio.Rmd

Scope

Compute the kynurenine/tryptophan ratio (KTR), a marker of IDO activity and immune activation. Supports NA policies, optional extreme screening (warn/cap/NA/error), and verbose progress. Inputs must already be Kyn (nmol/L) and Trp (µmol/L); no unit conversion.

Load packages and demo data 

library(HealthMarkers)
library(tibble)

df <- tibble::tibble(
  Kyn_nM = c(1800, 2500, 3200),
  Trp_uM = c(50, 42, 12)
)

Column map (required) 

col_map <- list(kynurenine = "Kyn_nM", tryptophan = "Trp_uM")

Core calculation

Default na_action = "keep": ratios are NA where inputs are missing; no extreme scan.

ktr <- kyn_trp_ratio(
  data = df,
  col_map = col_map,
  na_action = "keep",
  check_extreme = FALSE,
  verbose = FALSE
)

ktr
#> # A tibble: 3 × 1
#>   kyn_trp_ratio
#>           <dbl>
#> 1          36  
#> 2          59.5
#> 3         267.

Extreme screening

Scan and cap into default ranges.

df_ext <- df
df_ext$Kyn_nM[2] <- 50000  # extreme

ktr_cap <- kyn_trp_ratio(
  data = df_ext,
  col_map = col_map,
  na_action = "warn",
  check_extreme = TRUE,
  extreme_action = "cap",
  verbose = TRUE
)

ktr_cap
#> # A tibble: 3 × 1
#>   kyn_trp_ratio
#>           <dbl>
#> 1           36 
#> 2          476.
#> 3          267.

extreme_action = "warn" only warns; error aborts; NA blanks flagged values.

Missing data handling

keep/ignore/warn retain rows with NA ratios; omit drops rows with missing inputs; error stops on missingness.

df_na <- df
df_na$Trp_uM[3] <- NA

keep_out <- kyn_trp_ratio(df_na, col_map, na_action = "keep")
omit_out <- kyn_trp_ratio(df_na, col_map, na_action = "omit")

list(keep_rows = nrow(keep_out), omit_rows = nrow(omit_out))
#> $keep_rows
#> [1] 3
#> 
#> $omit_rows
#> [1] 2

Expectations

  • Both markers must be mapped and present; non-numeric inputs are coerced with warnings if NAs are introduced.
  • Trp must be positive; nonpositive values are set to NA with a warning.
  • Extreme defaults: Kyn 100–20000 nmol/L, Trp 10–150 µmol/L, ratio 0–200; adjust with extreme_rules.
  • Output: one-column tibble kyn_trp_ratio; row count follows na_action if you omit rows.

Verbose diagnostics 

old_opt <- options(healthmarkers.verbose = "inform")
kyn_trp_ratio(
  data    = df,
  col_map = col_map,
  verbose = TRUE
)
#> kyn_trp_ratio(): preparing inputs
#> kyn_trp_ratio(): column map: kynurenine -> 'Kyn_nM', tryptophan -> 'Trp_uM'
#> kyn_trp_ratio(): results: kyn_trp_ratio 3/3
#> # A tibble: 3 × 1
#>   kyn_trp_ratio
#>           <dbl>
#> 1          36  
#> 2          59.5
#> 3         267.
options(old_opt)

Tips

  • Re-check units when ratios are very high (>100); Kyn should be nmol/L and Trp µmol/L.
  • Use extreme_action = "cap" sparingly and adjust ranges to your cohort.
  • For modeling, consider scaling/transforming KTR separately after computation.