globalAdjPval: Computes the adjusted p-values on all the stacked contrasts...

In prostarproteomics/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

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

Description

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(s)

Thomas Burger

Examples

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

prostarproteomics/DAPAR documentation built on Oct. 11, 2024, 12:03 p.m.