A function to rank combinations by a Youden index and select them if they have a min SE and/or SP.
Arguments
- combo_table
a data.frame with SE, SP and number of composing markers for each combination (returned by se_sp()).
- min_SE
a numeric that specifies the min value of SE that a combination must have to be filtered-in.
- min_SP
a numeric that specifies the min value of SP that a combination must have to be filtered-in.
Value
a named list containing:
$table, a data.frame with ranked combination, reporting: SE, SP, number of markers composing the combination and the score.
$bubble_chart, a dot plot showing the selected 'gold' combinations
Details
This function is meant to help the user in finding the best combinations (in the first rows) and allows also (not mandatory) the SE/SP-dependent filtering of combinations.
Examples
if (FALSE) {
demo_data # combiroc built-in demo data (proteomics data from Zingaretti et al. 2012 - PMC3518104)
combs <- combi(data= demo_data, signalthr=450, combithr=1, case_class='A') # compute combinations
# compute SE and SP
# of each combination
# To rank combinations by Youden index and filter-out the ones with SE < min_SE and SP < min_SP
rc <- ranked_combs(combo_table= combs, min_SE=40, min_SP=80)
rc$table # to visualize the selected gold combinations through a data.frame
rc$bubble_chart # to visualize the selected gold combinations through a data.frame
}