computeRegionSignificance: Compute significance for given regions
In GenoGAM: A GAM based framework for analysis of ChIP-Seq data

Description Usage Arguments Details Value Author(s) Examples

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

1	computeRegionSignificance(fit, regions, smooth = NULL)

`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)`

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.

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

Georg Stricker georg.stricker@in.tum.de

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