ranked_combs {combiroc} | R Documentation |
Rank combinations.
Description
A function to rank combinations by a Youden index and select them if they have a min SE and/or SP.
Usage
ranked_combs(combo_table, min_SE = 0, min_SP = 0)
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. |
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.
Value
a named list containing:
$table, a data.frame with ranked combination, reporting: SE, SP, number of markers composing the combination and the score.
$bubble_chart, a dot plot showing the selected 'gold' combinations
Examples
## Not run:
demo_data # combiroc built-in demo data (proteomics data from Zingaretti et al. 2012 - PMC3518104)
combs <- combi(data= demo_data, signalthr=450, combithr=1, case_class='A') # compute combinations
# compute SE and SP
# of each combination
# To rank combinations by Youden index and filter-out the ones with SE < min_SE and SP < min_SP
rc <- ranked_combs(combo_table= combs, min_SE=40, min_SP=80)
rc$table # to visualize the selected gold combinations through a data.frame
rc$bubble_chart # to visualize the selected gold combinations through a data.frame
## End(Not run)