Hello all,
As the title says, are there any methods / tools available to estimate approximate age of a donor from 450k DNA methylation data. I found the following resource to start with but it has too many bugs and it's not running properly with their example datasets, I spent a lot of time debugging it but couldn't succeed.
DNA methylation age and the epigenetic clock
I would appreciate, if someone could direct me to some resources.
Thank you !
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venu
1 answer
The R code that you are supposed to run is within the Word / PDF files, which call the other files under "R Tutorials"
At the beginning of the extracted R code, you'll need to define dat0 as the beta matrix (such as dat0 = read.table("probe_beta.txt",head=T, sep="\t"))
Also, at least with the EPIC array, you'll have to modify that code to consider only probes that are on later array versions.
I got the code to work with the following modifications:
1) After datClock=read.csv("AdditionalFile3.csv"), add datClock = datClock[match(dat0[,1],datClock[,1],nomatch=0),]
2) Replace match1=match(probeAnnotation21kdatMethUsed$Name , dat0[,1]) with match1=match(probeAnnotation21kdatMethUsed$Name , dat0[,1], nomatch=0)
3) After dat1= dat0[match1,], add probeAnnotation21kdatMethUsed = probeAnnotation21kdatMethUsed[match(dat1[,1],probeAnnotation21kdatMethUsed$Name),]
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