santanalele
commented
3 years ago Hi aciolfi,
I was having the same issue and this is how I managed to fix it. So I basically created a new function to run DMRcate. I've commented below the lines of code which I found issues while debugging it.
DMRcate_manual_run = function(beta_matrix,
pheno,
arraytype,
dist = 2,
mafcut = 0.05,
fdr = 0.05,
lambda = 1000,
C = 2)
{
require(DMRcate)
myMs <- logit2(beta_matrix)
myMs <- rmSNPandCH(myMs, dist = dist, mafcut = mafcut)
design <- model.matrix(~ pheno)
if(arraytype == "450K"){
myannotation <- cpg.annotate(datatype = "array",
fdr = 0.05,
myMs,
design = design,
coef = ncol(design),
analysis.type = "differential",
annotation = c(array = "IlluminaHumanMethylation450k",
annotation = "ilmn12.hg19"),
what = "M")
} else {
myannotation <- cpg.annotate(datatype = "array",
fdr = 0.05,
myMs,
design = design,
coef = ncol(design),
analysis.type = "differential",
annotation = c(array = "IlluminaHumanMethylationEPIC",
annotation = "ilm10b4.hg19"),
what = "M")
}
#commenting lines with issues
# M <- do.call("cbind", lapply(myannotation, as.data.frame)) #don't know why this code is here
# colnames(M) <- names(myannotation) #don't know why this code is here
#removed unused mc.cores argument
dmrcoutput <- dmrcate(myannotation, lambda = lambda, C = C) #mc.cores = cores - this argument no longer applies
#data(dmrcatedata) - unsused line of code
DMR <- as.data.frame(extractRanges(dmrcoutput, genome = "hg19"))
rownames(DMR) <- paste("DMR", 1:nrow(DMR), sep="_")
message("DMRcate detected ", nrow(DMR)," DMRs with mafcut as = ", mafcut, ".")
if(nrow(DMR) == 0)
stop("No DMR detected.")
return(DMR)
}
#to run
DMRs <- DMRcate_manual_run(beta_matrix, pheno, "EPIC")
aciolfi
ClaireXinSun
ehugos
chiaracapp
valderpan
Hi Tian, I cannot use champ.DMR with DMRcate method, since I always receive the same error:
Here's my sessionInfo:
Could you please help me to understand what is going wrong? Thank you