Question: "MethylKit" package for WGBS data
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gravatar for shrinka.genetics
4 months ago by
shrinka.genetics0 wrote:

Hello I am working on WGBS data using MethylKIT package. I am trying to analyse few samples whose dimension are not same (see below). What kind of measure can be taken to handle this type of problem

library(methylKit) file.list = list ("JChr21-modd.txt","SChr21-modd.txt","Delta21-mod.txt","BChr21-modd.txt","NChr21-modd.txt") myobj = methRead (file.list, sample.id = list ("JChr21-modd","SChr21-modd","Delta21-mod", "BChr21-modd", "NChr21-modd"), assembly = "hg19", treatment = c(1,1,0,0,0), context = "CpG") meth=unite(myobj, destrand=FALSE) uniting... Error in unite(myobj, destrand = FALSE) : no base were united. try adjusting 'min.per.group’.

dim(Jchr21)

[1] 857692 6

dim(Delta21)

[1] 760888 6

sequencing next-gen • 184 views
ADD COMMENTlink written 4 months ago by shrinka.genetics0

You are posting these kinds of question for weeks (maybe months now), don't you think it is time to talk to someone who can guide you at your institution locally, given that you have trouble all the way? Online communities are great for specific questions but hands-on guidance which are apparently need at this point is not in the scope of them. I really say this in your best interest.

ADD REPLYlink modified 4 months ago • written 4 months ago by ATpoint44k

It seems methylkit was not able to find anything common between 5 samples. Is your input file tab delimited? If yes try providing seperator as sep = "\t" .

ADD REPLYlink written 4 months ago by toralmanvar900
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