Update p values according multiple comparisons
padjustCompareGroups.RdGiven a compareGroups object, returns their p-values adjusted using one of several methods (stats::p.adjust)
Arguments
- object_compare
object of class
compareGroups- p
character string. Specify which p-value must be corrected. Possible values are 'p.overall' and 'p.trend' (default: 'p.overall')
- method
Correction method, a character string. Can be abbreviated (see
p.adjust).
Examples
# Define simulated data
set.seed(123)
N_obs<-100
N_vars<-50
data<-matrix(rnorm(N_obs*N_vars), N_obs, N_vars)
sim_data<-data.frame(data,Y=rbinom(N_obs,1,0.5))
# Execute compareGroups
res<-compareGroups(Y~.,data=sim_data)
res
#>
#>
#> -------- Summary of results by groups of 'Y'---------
#>
#>
#> var N p.value method selection
#> 1 X1 100 0.859 continuous normal ALL
#> 2 X2 100 0.729 continuous normal ALL
#> 3 X3 100 0.882 continuous normal ALL
#> 4 X4 100 0.322 continuous normal ALL
#> 5 X5 100 0.115 continuous normal ALL
#> 6 X6 100 0.878 continuous normal ALL
#> 7 X7 100 0.663 continuous normal ALL
#> 8 X8 100 0.064* continuous normal ALL
#> 9 X9 100 0.971 continuous normal ALL
#> 10 X10 100 0.828 continuous normal ALL
#> 11 X11 100 0.494 continuous normal ALL
#> 12 X12 100 0.521 continuous normal ALL
#> 13 X13 100 0.404 continuous normal ALL
#> 14 X14 100 0.539 continuous normal ALL
#> 15 X15 100 0.723 continuous normal ALL
#> 16 X16 100 0.828 continuous normal ALL
#> 17 X17 100 0.133 continuous normal ALL
#> 18 X18 100 0.442 continuous normal ALL
#> 19 X19 100 0.869 continuous normal ALL
#> 20 X20 100 0.332 continuous normal ALL
#> 21 X21 100 0.497 continuous normal ALL
#> 22 X22 100 0.132 continuous normal ALL
#> 23 X23 100 0.091* continuous normal ALL
#> 24 X24 100 0.005** continuous normal ALL
#> 25 X25 100 0.369 continuous normal ALL
#> 26 X26 100 0.134 continuous normal ALL
#> 27 X27 100 0.063* continuous normal ALL
#> 28 X28 100 0.791 continuous normal ALL
#> 29 X29 100 0.235 continuous normal ALL
#> 30 X30 100 0.928 continuous normal ALL
#> 31 X31 100 0.923 continuous normal ALL
#> 32 X32 100 0.436 continuous normal ALL
#> 33 X33 100 0.827 continuous normal ALL
#> 34 X34 100 0.234 continuous normal ALL
#> 35 X35 100 0.433 continuous normal ALL
#> 36 X36 100 0.121 continuous normal ALL
#> 37 X37 100 0.555 continuous normal ALL
#> 38 X38 100 0.415 continuous normal ALL
#> 39 X39 100 0.905 continuous normal ALL
#> 40 X40 100 0.897 continuous normal ALL
#> 41 X41 100 0.095* continuous normal ALL
#> 42 X42 100 0.601 continuous normal ALL
#> 43 X43 100 0.003** continuous normal ALL
#> 44 X44 100 0.224 continuous normal ALL
#> 45 X45 100 0.303 continuous normal ALL
#> 46 X46 100 0.324 continuous normal ALL
#> 47 X47 100 0.720 continuous normal ALL
#> 48 X48 100 0.017** continuous normal ALL
#> 49 X49 100 0.233 continuous normal ALL
#> 50 X50 100 0.852 continuous normal ALL
#> -----
#> Signif. codes: 0 '**' 0.05 '*' 0.1 ' ' 1
#>
# update p values
res_adjusted<-padjustCompareGroups(res)
res_adjusted
#>
#>
#> -------- Summary of results by groups of 'Y'---------
#>
#>
#> var N p.value method selection
#> 1 X1 100 0.947 continuous normal ALL
#> 2 X2 100 0.947 continuous normal ALL
#> 3 X3 100 0.947 continuous normal ALL
#> 4 X4 100 0.831 continuous normal ALL
#> 5 X5 100 0.557 continuous normal ALL
#> 6 X6 100 0.947 continuous normal ALL
#> 7 X7 100 0.947 continuous normal ALL
#> 8 X8 100 0.557 continuous normal ALL
#> 9 X9 100 0.971 continuous normal ALL
#> 10 X10 100 0.947 continuous normal ALL
#> 11 X11 100 0.887 continuous normal ALL
#> 12 X12 100 0.896 continuous normal ALL
#> 13 X13 100 0.850 continuous normal ALL
#> 14 X14 100 0.896 continuous normal ALL
#> 15 X15 100 0.947 continuous normal ALL
#> 16 X16 100 0.947 continuous normal ALL
#> 17 X17 100 0.557 continuous normal ALL
#> 18 X18 100 0.850 continuous normal ALL
#> 19 X19 100 0.947 continuous normal ALL
#> 20 X20 100 0.831 continuous normal ALL
#> 21 X21 100 0.887 continuous normal ALL
#> 22 X22 100 0.557 continuous normal ALL
#> 23 X23 100 0.557 continuous normal ALL
#> 24 X24 100 0.135 continuous normal ALL
#> 25 X25 100 0.850 continuous normal ALL
#> 26 X26 100 0.557 continuous normal ALL
#> 27 X27 100 0.557 continuous normal ALL
#> 28 X28 100 0.947 continuous normal ALL
#> 29 X29 100 0.733 continuous normal ALL
#> 30 X30 100 0.947 continuous normal ALL
#> 31 X31 100 0.947 continuous normal ALL
#> 32 X32 100 0.850 continuous normal ALL
#> 33 X33 100 0.947 continuous normal ALL
#> 34 X34 100 0.733 continuous normal ALL
#> 35 X35 100 0.850 continuous normal ALL
#> 36 X36 100 0.557 continuous normal ALL
#> 37 X37 100 0.896 continuous normal ALL
#> 38 X38 100 0.850 continuous normal ALL
#> 39 X39 100 0.947 continuous normal ALL
#> 40 X40 100 0.947 continuous normal ALL
#> 41 X41 100 0.557 continuous normal ALL
#> 42 X42 100 0.939 continuous normal ALL
#> 43 X43 100 0.135 continuous normal ALL
#> 44 X44 100 0.733 continuous normal ALL
#> 45 X45 100 0.831 continuous normal ALL
#> 46 X46 100 0.831 continuous normal ALL
#> 47 X47 100 0.947 continuous normal ALL
#> 48 X48 100 0.288 continuous normal ALL
#> 49 X49 100 0.733 continuous normal ALL
#> 50 X50 100 0.947 continuous normal ALL
#> -----
#> Signif. codes: 0 '**' 0.05 '*' 0.1 ' ' 1
#>
# update p values using FDR method
res_adjusted<-padjustCompareGroups(res, method ="fdr")
res_adjusted
#>
#>
#> -------- Summary of results by groups of 'Y'---------
#>
#>
#> var N p.value method selection
#> 1 X1 100 0.947 continuous normal ALL
#> 2 X2 100 0.947 continuous normal ALL
#> 3 X3 100 0.947 continuous normal ALL
#> 4 X4 100 0.831 continuous normal ALL
#> 5 X5 100 0.557 continuous normal ALL
#> 6 X6 100 0.947 continuous normal ALL
#> 7 X7 100 0.947 continuous normal ALL
#> 8 X8 100 0.557 continuous normal ALL
#> 9 X9 100 0.971 continuous normal ALL
#> 10 X10 100 0.947 continuous normal ALL
#> 11 X11 100 0.887 continuous normal ALL
#> 12 X12 100 0.896 continuous normal ALL
#> 13 X13 100 0.850 continuous normal ALL
#> 14 X14 100 0.896 continuous normal ALL
#> 15 X15 100 0.947 continuous normal ALL
#> 16 X16 100 0.947 continuous normal ALL
#> 17 X17 100 0.557 continuous normal ALL
#> 18 X18 100 0.850 continuous normal ALL
#> 19 X19 100 0.947 continuous normal ALL
#> 20 X20 100 0.831 continuous normal ALL
#> 21 X21 100 0.887 continuous normal ALL
#> 22 X22 100 0.557 continuous normal ALL
#> 23 X23 100 0.557 continuous normal ALL
#> 24 X24 100 0.135 continuous normal ALL
#> 25 X25 100 0.850 continuous normal ALL
#> 26 X26 100 0.557 continuous normal ALL
#> 27 X27 100 0.557 continuous normal ALL
#> 28 X28 100 0.947 continuous normal ALL
#> 29 X29 100 0.733 continuous normal ALL
#> 30 X30 100 0.947 continuous normal ALL
#> 31 X31 100 0.947 continuous normal ALL
#> 32 X32 100 0.850 continuous normal ALL
#> 33 X33 100 0.947 continuous normal ALL
#> 34 X34 100 0.733 continuous normal ALL
#> 35 X35 100 0.850 continuous normal ALL
#> 36 X36 100 0.557 continuous normal ALL
#> 37 X37 100 0.896 continuous normal ALL
#> 38 X38 100 0.850 continuous normal ALL
#> 39 X39 100 0.947 continuous normal ALL
#> 40 X40 100 0.947 continuous normal ALL
#> 41 X41 100 0.557 continuous normal ALL
#> 42 X42 100 0.939 continuous normal ALL
#> 43 X43 100 0.135 continuous normal ALL
#> 44 X44 100 0.733 continuous normal ALL
#> 45 X45 100 0.831 continuous normal ALL
#> 46 X46 100 0.831 continuous normal ALL
#> 47 X47 100 0.947 continuous normal ALL
#> 48 X48 100 0.288 continuous normal ALL
#> 49 X49 100 0.733 continuous normal ALL
#> 50 X50 100 0.947 continuous normal ALL
#> -----
#> Signif. codes: 0 '**' 0.05 '*' 0.1 ' ' 1
#>