Function to calculate the sensitivity and specificity of a genetic distance cutoff given an underlying mutation rate and mean number of generations between cases

sens_spec_calc(
  cutoff,
  mut_rate,
  mean_gens_pdf,
  max_link_gens = 1,
  max_gens = NULL,
  max_dist = NULL
)

Arguments

cutoff

the maximum genetic distance at which to consider cases linked

mut_rate

mean number of mutations per generation, assumed to be poisson distributed

mean_gens_pdf

the density distribution of the mean number of generations between cases; the index of this vector is assumed to be the discrete distance between cases

max_link_gens

the maximium generations of separation for linked pairs

max_gens

the maximum number of generations to consider, if NULL (default) value set to the highest number of generations in mean_gens_pdf with a non-zero probability

max_dist

the maximum distance to calculate, if NULL (default) value set to max_gens * 99.9th percentile of mut_rate poisson distribution

Value

a data frame with the sensitivity and specificity for a particular genetic distance cutoff

See also

Other mutrate_functions: gen_dists(), get_optim_roc(), sens_spec_roc()

Author

Shirlee Wohl and Justin Lessler

Examples

# calculate the sensitivity and specificity for a specific genetic distance threshold of 2 mutations sens_spec_calc(cutoff=2, mut_rate=1, mean_gens_pdf=c(0.02,0.08,0.15,0.75), max_link_gens=1)
#> cutoff sensitivity specificity #> [1,] 2 0.7357589 0.8662894
# calculate the sensitivity and specificity for a a range of genetic distance thresholds sens_spec_calc(cutoff=1:10, mut_rate=1, mean_gens_pdf=c(0.02,0.08,0.15,0.75), max_link_gens=1)
#> cutoff sensitivity specificity #> [1,] 1 0.3678794 0.967314682 #> [2,] 2 0.7357589 0.866289434 #> [3,] 3 0.9196986 0.697765199 #> [4,] 4 0.9810118 0.499227295 #> [5,] 5 0.9963402 0.316627604 #> [6,] 6 0.9994058 0.178637743 #> [7,] 7 0.9999168 0.090198436 #> [8,] 8 0.9999898 0.041044514 #> [9,] 9 0.9999989 0.016951040 #> [10,] 10 0.9999999 0.006396198