Repitools (version 1.18.0)

maskOut: Function to mask suspicious regions.

Description

Function to mask out regions that are prone to causing problems in the empirical Bayes approach empBayes. The corresponding bins are marked and in the empirical Bayes approach not taken into account. Notice that methylation estimates using methylEst will nevertheless be produced for these bins.

Usage

maskOut(x, ranges)

Arguments

x

Object of class BayMethList.

ranges

A GRanges object definining the coordinates of regions to be masked out.

Value

A BayMethList object where the slot maskout is filled with a boolean vector indicating which bins will be excluded in empBayes.

Examples

    if(require(BSgenome.Hsapiens.UCSC.hg18)){
        windows <- genomeBlocks(Hsapiens, chrs="chr21", width=100, spacing=100)
        cpgdens <- cpgDensityCalc(windows, organism=Hsapiens, 
            w.function="linear", window=700)  
        co <- matrix(rnbinom(length(windows), mu=10, size=2), ncol=1)
        sI <- matrix(rnbinom(2*length(windows), mu=5, size=2), ncol=2)
        bm <- BayMethList(windows=windows, control=co, 
            sampleInterest=sI, cpgDens=cpgdens)

        # mask out unannotated high copy number regions
        # see Pickrell et al. (2011), Bioinformatics 27: 2144-2146.
        data(hcRegions)

        bm <- maskOut(bm, hcRegions)
   }