maskOut {Repitools} | R Documentation |
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.
maskOut(x, ranges)
x |
Object of class |
ranges |
A GRanges object definining the coordinates of regions to be masked out. |
A BayMethList
object where the slot maskout
is filled with a
boolean vector indicating which bins will be excluded in empBayes
.
Andrea Riebler
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) }