adjustPvalGSE {RTopper} | R Documentation

## 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

### 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.

### 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

### Author(s)

Luigi Marchionni marchion@jh.edu

### 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")

[Package RTopper version 1.26.0 Index]