RTopper (version 1.18.0)

adjustPvalGSE: Multiple testing correction

Description

This function is an interface to the mt.rawp2adjp function contained in the multtest package. adjustPvalGSE works on outputs from runBatchGSE and combineGSE returning adjusted p-values

Usage

adjustPvalGSE(gseOut, proc = "BH", alpha = 0.05 , na.rm = FALSE)

Arguments

gseOut

list of lists, either the output from runBatchGSE, or the output from combineGSE

proc

character, the method to be used for p-values adjusting. This parameter will be passed to the mt.rawp2adjp function from the multtest package. The available options include: "Bonferroni", "Holm", "Hochberg", "SidakSS", code"SidakSD", "BH" (the default), "BY", "ABH", and "TSBH"

alpha

numeric, the nominal type I error rate

na.rm

logical, the option for handling NA values in the list of raw p-values

Value

For each vector of p-value contained in the gseOut input object a data.frame is returned, containing original p-value and corrected p-values

Details

The adjustPvalGSE function performs p-value adjusting for multiple testing correction on the list of lists resulting from enrichment analysis obtained using the runBatchGSE and combineGSE functions. This functions is based on the mt.rawp2adjp function contained in the multtest package.

References

Svitlana Tyekucheva, Luigi Marchionni, Rachel Karchin, and Giovanni Parmigiani. "Integrating diverse genomic data using gene sets." Manuscript submitted.

Examples

###load gse analysis results for separate gene-to-phenotype score
data(gseResultsSep)

###adjust for multiple testing using the Benjamini and Hochberg method
gseABS.int.BH <- adjustPvalGSE(gseResultsSep)

###adjust for multiple testing using the Holm method
gseABS.int.holm <- adjustPvalGSE(gseResultsSep, proc = "Holm")