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

Someone could you please give me clue about "extdata", when people use "MethylKit" package in R for Whole Genome Bisulphite Sequencing (WGBS data)

next-gen • 114 views
ADD COMMENTlink modified 24 days ago • written 4 weeks ago by shrinka.genetics0

extdata are example data the package authors provide to run their functions. You do not need this and have to replace it with your own data. If you want more details you have to me more specific.

ADD REPLYlink written 4 weeks ago by ATpoint31k

Thank you I have used this code, like

library(methylKit)

file.list = list ("file1.txt", "file2.txt")

myobj = methRead (file.list, sample.id = list ("file1", "file2"), assembly = "hg19", pipeline = "bismarkCoverage",treatment = c(1,0), context = "CpG")

myobj was passed……………………………

meth=unite(myobj, destrand=FALSE)

uniting...

Error in vecseq(f__, len__, if (allow.cartesian || notjoin || !anyDuplicated(f__, :

Join results in 1880 rows; more than 87 = nrow(x)+nrow(i). Check for duplicate key values in i each of which join to the same group in x over and over again. If that's ok, try by=.EACHI to run j for each group to avoid the large allocation. If you are sure you wish to proceed, rerun with allow.cartesian=TRUE. Otherwise, please search for this error message in the FAQ, Wiki, Stack Overflow and data.table issue tracker for advice.

Any clue? Why I am getting this error?

ADD REPLYlink written 24 days ago by shrinka.genetics0
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