error while running DMRcate
1
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Entering edit mode
Jitendra ▴ 10
@nabiyogesh-11718
Last seen 15 hours ago
United Kingdom

Hi all,

I am getting an error while running DMRcate code below;

 Error in rmSNPandCH(mval, dist = 2, mafcut = 0.05) : 
      is.matrix(object) is not TRUE
    Calls: rmSNPandCH -> stopifnot
    Execution halted

DMRcate code

library("data.table")
#phenotype file
targets<-read.table("Limma.phenotypes.txt", header=TRUE, stringsAsFactor=FALSE,row.names=NULL, sep="\t")
head(targets)

#convert eGFR into  log 2

targets$logeGFR=log2(targets$eGFR)

#set first column header as blanck

names(targets)[1] <- ""

# first column as row names
targets2<-targets[,-1]
rownames(targets2)<-targets[,1]

head(targets2)
dim(targets2)

#read mehtylation data

###################



#Start by inputting your original beta value file, skipping any of the first few columns we don't need for this analysis (easily done in preview import)

betaval <- read_csv("betas_1.csv", col_types = cols(Chromosome = col_skip(), Start = col_skip(), End = col_skip(), Strand = col_skip()))




head(betaval, 10) [,1:5]

#set first column header as blank
names(betaval)[1] <- ""

#convert into dataframe
betaval <- data.frame(betaval)
# first column as row names

betaval2<-betaval[,-1]
rownames(betaval2)<-betaval[,1]

#convert beta value into m value
mval<-log2(betaval2/(1-betaval2))


dim(mval)

head(mval, 10) [,1:5]



library(DMRcate)


myMs.noSNPs <- rmSNPandCH(mval, dist=2, mafcut=0.05)

design <- model.matrix(~logeGFR + as.factor(Gender) + Age +CD8T +CD4T +NK + Bcell +Mono ,data=targets2)

myannotation <- cpg.annotate(myMs.noSNPs, analysis.type="differential",design=design, coef=2, contrats=FALSE)
dmrcoutput <- dmrcate(myannotation, lambda=1000, C=2)
results.ranges <- extractRanges(dmrcoutput, genome = "hg19")
stattistics epicarray Epigenetics DMRcate • 504 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

Yes, and the error seems self-explanatory?

Error in rmSNPandCH(mval, dist = 2, mafcut = 0.05) : 
      is.matrix(object) is not TRUE

Reading the help page will tell you that object is the first argument.

0
Entering edit mode

thanks @James, what would be best way to convert mval into matrix? I am just using this

# Converting into numeric matrix 
mval <- data.matrix(mval)
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0
Entering edit mode

That or as.matrix. Your call.

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0
Entering edit mode

thanks James, all sorted now I got DMRcate out file, could you please help how to use CHiPpeakAnno or CHiPseeker for further analysis?

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Both of those packages have extensive vignettes that you can consult.

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