Nothing
get_all_DMRs <- function(chromDictObj, seeds, res=40, max.dmr.size=3000, min.dmr.cpgs=10, min.absZscore, null){
while(length(seeds) > 0){
d <- oneSeed(chromDictObj, seeds[1], resolution = res, max.size = max.dmr.size, mincpgs = min.dmr.cpgs, null_list=null)
seeds <- seeds[-c(1)]
if(is.character(d)){
if(d=="FAIL"){
warning("Cannot calculate DMRs!")
}
} else{
if(exists("outputfile")==F){
outputfile <- d[[1]]
output_regions <- list(d[[2]])
} else{
outputfile <- rbind(outputfile, d[[1]])
output_regions <- append(output_regions, list(d[[2]]))
}
rm(d)
}
}
outputfile$DMR_size <- outputfile$end-outputfile$start
return(list(outputfile, output_regions))
}
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