DMRcate: How to get Cpgids present in the DMR

Question

[bassanio]

Hi,

The below is my Dmrcate run and I do get the DMRS. but how to get the CPGids that are part of these DMRS

corfit <- duplicateCorrelation(myMs, design=designMatrix, block = biolrep)
dmrCate.<-cpg.annotate("array", myMs, what="M", arraytype = "EPIC", analysis.type="differential", design=designMatrix, coef=2, block=biolrep, correlation=corfit$consensus.correlation,fdr=0.01)
dmrcoutput_all <- dmrcate(dmrCate,lambda=500, C=5, pcutoff="fdr",min.cpgs=1,mc.cores=1)
wgbs.ranges_all.snp7 <- extractRanges(dmrcoutput_all, genome = "hg19")
write.csv (wgbs.ranges_all.snp7,file="DMRCate_DifferentailRange.txt")
write.csv(dmrcoutput_all.snp7$results,file="DMRCate_ALL.txt")

how to get the 17 Cpgids from the result shown below

"","seqnames","start","end","width","strand","no.cpgs","minfdr","Stouffer","maxbetafc","meanbetafc","overlapping.promoters"
"1","chr6",31539539,31540750,1212,"*",17,2.06654851019045e-120,2.16758469969414e-149,-0.162022961391297,-0.106211449278892,"LTA-001, LTA-002, LTA-004, LTA-003"

I tried with gRanges but unable to understand how to perform it

P.S: I have posted the same in Bioconductor Forum. sorry for redundancy. Any help soon is appriciated

Answer 1

[bassanio]

gr <- granges(OBJECT)
locs.ranges<-names(gr[seqnames(gr) == "chr6" & start(gr)>=31539539 & end(gr) <=31540750 ])

The above two lines I was able to subset the ids belonging to 1 location of interest. How can I loop this multiple locations present in a dataframe?

Answer 2

[bassanio]

There would be multiple ways(more efficient way ) to what do than the below script which I have used solve my own problem.

But It would be great to know If there is any efficient way to do the same.

OBJECT <- is the last object from which beta/mvalue for DMRCate is give as input

gr <- granges(OBJECT)

    mydata<-read.csv(file="DMRCate_Output.csv",header=TRUE,stringsAsFactors = FALSE)
    for(n in 1:nrow(mydata))
    {
      chr<-mydata2[n,2]
      start=mydata2[n,3]
      end=mydata2[n,4]
      infos<-names(gr[seqnames(gr) == chr & start(gr)>=start & end(gr) <=end ])
      allcpg<-toString(infos)
      mydata$cpgids<-allcpg
    }

    write.table(mydata,file="DMRCate_Model3_DifferentailRange_V3V4_withCpgids",sep="\t");

P.S: Here the output from DMRcate is written to a file