DMRcate: Cpgids in DMR
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@yoursbassanio-12717
Last seen 10 months ago

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

methylation Epic annotation DMRcate • 275 views
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 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.

But now How can I loop this for multiple locations present in a data.frame of dmrcoutput_all?

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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)

 #read DMRcate outputstringsAsFactors = FALSE ;else there issue by creating levels
 mydata<-read.csv(file="DMRCate_Output.csv",header=TRUE,stringsAsFactors = FALSE)  

    for(n in 1:nrow(mydata)) 
    {

      # chr is the second column
      chr<-mydata2[n,2]   

      # DMR start is in 3rd column
       start=mydata2[n,3]   

       #DMR end is in 4th column
       end=mydata2[n,4]   

     #strand where all "*" so not included while retrieving
      #Start and end pos included 
      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

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Entering edit mode
 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 for multiple locations present in a data.frame of dmrcoutput_all?

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@james-w-macdonald-5106
Last seen 19 hours ago
United States

You don't say what your starting object is, so you are asking us to read your mind. If I were to do so, I would divine that you used minfi to import and process your data, and you have a GenomicRatioSet that you got your M-values from. And since that's obviously what you did, you can just do

firstrow <- subsetByOverlaps(OBJECT, wgbs.ranges_all.snp7[1,])

Which will give you a GenomicRatioSet that only contains the data that overlap the first DMR. Which you can do things with. Also, read the vignettes for GenomicRanges.

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Also, if you aren't answering your own question (which it appears you weren't?), don't use the Add your answer box, but instead ADD REPLY or ADD COMMENT.

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