computeRegionSignificance: Compute significance for given regions

Description Usage Arguments Details Value Author(s) Examples

View source: R/diffBinding.R

Description

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

Usage

1

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 [email protected]

Examples

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

GenoGAM documentation built on Dec. 7, 2018, 6 p.m.