computeRegionSignificance {GenoGAM} | R Documentation

## Compute significance for given regions

### Description

For a given set of regions, region-wise pvalues and FDR is computed

### Usage

    computeRegionSignificance(fit, regions, what = NULL)

### Arguments

`fit` | A GenoGAM object containing the fit
`regions` | A GRanges object of regions of interest
`what` | Which fit should be used. The names should be equivalent to the column names used in the config file. Lookup with `names(colData(my_GenoGAMDataSet_object))`

### Details

For a given set of regions, region-wise pvalues are computed by applying familywise hochberg correction and taking the minimal p-value. FDR is computed by further applying Benjamini-Hochberg correction.

### Value

The GRanges object from the 'region' parameter extended by two columns: pvalue and FDR

### Author(s)

Georg Stricker georg.stricker@in.tum.de

### Examples

    gg <- makeTestGenoGAM()
    gr <- GRanges("chrI", IRanges(1,100))
    computeRegionSignificance(gg, gr)

[Package GenoGAM version 1.8.0 Index]