"MethylKit" package for WGBS data

Question

[shrinka.genetics]

Hello I am working with WGBS data and using MethyKit package. I have 12 samples in 3 groups. I used codes like

> file.list = list ("JChr21-modd.txt", "BChr21-modd.txt", "SChr21-modd.txt", "NChr21-modd.txt","KChr21-modd.txt","EChr21-modd.txt","CChr21-modd.txt","PChr21-modd.txt", "IChr21-modd.txt","RChr21-modd.txt","LChr21-modd.txt","MChr21-modd.txt")

> myobj = methRead (file.list, sample.id = list ("JChr21-modd", "BChr21-modd", "SChr21-modd", "NChr21-modd","KChr21-modd","EChr21-modd", "CChr21-modd", "PChr21-modd","IChr21-modd","RChr21-modd", "LChr21-modd", "MChr21-modd"), assembly = "hg19", treatment = c(2,2,2,2,1,1,1,1,0,0,0,0), context = "CpG")

> meth=unite(myobj, destrand=FALSE)  uniting...

> PCASamples (meth)

Here they are giving me PC1 Vs PC2 plot. My question is how can I get PC1 Vs PC3, PC2 Vs PC3 etc others PCA plots, by changing arguments or what?

Thanks Shrinka

Answer 1

[Friederike]

My question is how can I get PC1 Vs PC3, PC2 Vs PC3 etc others PCA plots, by changing arguments or what?

Yes.

If you type ?PCASamples you should see the documentation of that function. This will explain that there is a comp parameter, which can be used to define the components to be plotted. Without having used the function I'll guess that that's what you're looking for.