globalAdjPval: Computes the adjusted p-values on all the stacked contrasts...
In prostarproteomics/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R
View source: R/anova_analysis.R
globalAdjPval R Documentation
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")$P_Value)
prostarproteomics/DAPAR documentation built on Nov. 26, 2024, 6:32 p.m.
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View source: R/anova_analysis.R
| globalAdjPval | R Documentation |
Computes the adjusted p-values on all the stacked contrasts using CP4P
Description
Computes the adjusted p-values on all the stacked contrasts using CP4P
Usage
globalAdjPval(x, pval.threshold = 1.05, method = 1, display = T)
Arguments
x |
a proteins x contrasts dataframe of (raw) p-values |
pval.threshold |
all the p-values above the threshold are not considered. Default is 1.05 (which is equivalent to have no threshold). Applying a threshold nearby 1 can be instrumental to improve the uniformity under the null, notably in case of upstream mutliple contrat correction (for experienced users only) |
method |
method a method to estimate pi_0, see CP4P |
display |
if T, a calibration plot is diplayed using CP4P |
Value
a proteins x contrasts table of adjusted p-values
Author(s)
Thomas Burger
Examples
data(Exp1_R25_prot, package='DAPARdata')
exdata <- Exp1_R25_prot[1:5,]
globalAdjPval(testAnovaModels(applyAnovasOnProteins(exdata), "TukeyHSD")$P_Value)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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