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]