computeRegionSignificance {GenoGAM} | R Documentation |
For a given set of regions, region-wise pvalues and FDR is computed
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 |
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