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, smooth = NULL)

### Arguments

`fit` | A GenoGAM object containing the fit
`regions` | A GRanges object of regions of interest
`smooth` | Which fit should be used. The names should be equivalent to the column names of the object. Lookup with `colnames(my_GenoGAM_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

    ## make test GenoGAM
    gg <- makeTestGenoGAM()
    ## make region
    region <- GRanges("chrXYZ", IRanges(c(2000, 4000, 6000), c(3000, 5000, 9000)))
    res <- computeRegionSignificance(gg, region)
    res

[Package GenoGAM version 2.2.0 Index]