I've been using bumphunter to get DMR and Blocks as defined in the ChAMP package (champ.DMR and champ.Block functions, respectively) on a MethylationEPIC data set (37 controls, 41 patients). Unfortunately, for both functions, it's stalling at:
[bumphunterEngine] Computing coefficients. [bumphunterEngine] Smoothing coefficients.
I've been running with at least 20 cores/100 GB memory for up to 99 hours. I've been trying R v. 3.5, 3.5.3, and 3.6. How can this smoothing take so long/any advice on what I should do? The last time, I tried with R v. 3.5 using ChAMP v. 2.12.4 (bumphunter v. 1.24.5). with standard code:
champ.DMR(beta=myNorm, pheno=myLoad$pd$Sample_Group, compare.group=NULL, arraytype="EPIC", method = "Bumphunter", minProbes=7, adjPvalDmr=0.05, cores=20, ## following parameters are specifically for Bumphunter method. maxGap=300, cutoff=NULL, pickCutoff=TRUE, smooth=TRUE, smoothFunction=loessByCluster, useWeights=FALSE, permutations=NULL, B=250, nullMethod="bootstrap")
[ Section 2: Run DMR Algorithm Start ] Loading required package: IlluminaHumanMethylationEPICanno.ilm10b4.hg19 << Find DMR with Bumphunter Method >> 20 cores will be used to do parallel Bumphunter computing. According to your data set, champ.DMR() detected 11355 clusters contains MORE THAN 7 probes within300 maxGap. These clusters will be used to find DMR. [bumphunterEngine] Parallelizing using 20 workers/cores (backend: doParallelMC, version: 1.0.14). [bumphunterEngine] Computing coefficients. [bumphunterEngine] Smoothing coefficients. Loading required package: rngtools Loading required package: pkgmaker Loading required package: registry Attaching package: 'pkgmaker' The following object is masked from 'package:S4Vectors': new2 The following object is masked from 'package:base': isFALSE =>> PBS: job killed: walltime 356440 exceeded limit 356400
I will add sessionInfo() later, server is busy right now.