Generation of Dendogram on WGBS data

Question

[shrinka.genetics]

Hi I am working on WGBS data and using MethylKit package. Methykit has its own function to make a dendogram on CpG methylation, but I need bootstraping on it. I used these codes.

library(methylKit) file.list = list (........) myobj = methRead (file.list, sample.id = list (..........), assembly = "hg19", treatment = c(), context = "CpG") meth=unite(myobj, destrand=FALSE) data<-clusterSamples(meth, dist= "correlation", method= "ward", plot=TRUE) library(pvclust) result <- pvclust(data, nboot=10000)

These are the usage of these arguments

1) clusterSamples(.Object, dist="correlation", method="ward", sd.filter=TRUE,sd.threshold=0.5, filterByQuantile=TRUE, plot=TRUE,chunk.size)

2) pvclust(data, method.hclust="average", method.dist="correlation", use.cor="pairwise.complete.obs", nboot=1000, parallel=FALSE, r=seq(.5,1.4,by=.1), store=FALSE, weight=FALSE, iseed=NULL, quiet=FALSE)

I have tried various ways, sometimes by putting meth directly or sometime that data object and tried it, but every time getting error something or other.

Anyone could you please help me regarding this? Any suggestion, that how can I modify my codes to have my result.

Answer 1

[iwwilson]

This article may be of use (I'm about to work through it myself). Check out Additional File 7 - they included the code used to pass MethylKit's dendrogram to pvclust:

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5578-4