Computes the adjusted p-values on all the stacked contrasts using CP4P

Usage

globalAdjPval(x, pval.threshold = 1.05, method = 1, display = T)

Arguments

x: a proteins x contrasts dataframe of (raw) p-values
pval.threshold: all the p-values above the threshold are not considered. Default is 1.05 (which is equivalent to have no threshold). Applying a threshold nearby 1 can be instrumental to improve the uniformity under the null, notably in case of upstream mutliple contrat correction (for experienced users only)
method: method a method to estimate pi_0, see CP4P
display: if T, a calibration plot is diplayed using CP4P

Value

a proteins x contrasts table of adjusted p-values

Author

Thomas Burger

Examples

data(Exp1_R25_prot, package='DaparToolshedData')
exdata <- Exp1_R25_prot[1:5,]
globalAdjPval(testAnovaModels(applyAnovasOnProteins(exdata, 1), "TukeyHSD")$P_Value)

#> Procedure of Benjamini-Hochberg is used. pi0 is fixed to 1.
#>                                                     V1_pval
#> CON__A2I7N1.CON__A2I7N0                        0.7209545661
#> CON__P00761                                    0.8916825703
#> P02768upsedyp.ALBU_HUMAN_upsedyp.CON__P02768.1 0.0001321402
#> CON__P04264                                    0.1253349546
#> CON__P07477                                    0.8916825703