[Methylkit]-Error in validObject(.Object) :
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liulip • 0
@liulip-20283
Last seen 16 months ago
China

Hi there,

I just got a problem with methRead function in the R package Methylkit, hope you guys can help me:)

This is my CpG dataset: enter image description here

My code is as followed:

setwd("/data/Users/llp/worl/RRBS/cov")

file.list=list("P1_1.txt","P1_2.txt","P7_1.txt","P7_2.txt")

myobj=methRead(file.list,
               sample.id=list("P1_1","P1_2","P7_1","P7_2"),
               assembly="mm10",
               treatment=c(0,0,1,1),
               context="CpG",
               mincov = 5)

Here is the wrong message I keep receiveing:

Error in validObject(.Object) : 
  invalid class “methylRaw” object: superclass "vector_OR_Vector" not defined in the environment of the object's class

Thank you very much in advance!

Elaine liu

methRead methylkit • 584 views
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I made it !

update S4Vectors from 0.20.0 to 0.24.4 & BiocGenerics from 0.30.0 to 0.32.0, it works~

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