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 )
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 |
max_dist | the maximum distance to calculate, if |
a data frame with the sensitivity and specificity for a particular genetic distance cutoff
Other mutrate_functions:
gen_dists()
,
get_optim_roc()
,
sens_spec_roc()
Shirlee Wohl and Justin Lessler
# 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