Help for resource: Estimating age from 450k DNA methylation data

Question

[venu]

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 !

Answer 1

[Charles Warden]

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),]

[venu]

Thanks for taking a look. I will check and update :)