Error in file.exists(filepath) : invalid 'file' argument

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In Ki Cho

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Oct 23, 2021, 12:34:38 PM10/23/21
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I am lost here. 
I ran alignment with BWA-Meth and got methylKit output from methylDackel. 
The output file has 7 columns 

chrBase, chr, base, strand, coverage, freqC, freqT

I imported the files into R and tried to run MethylKit, but once I created the file.list and run 

> myobj=methRead(file.list,
+                sample.id=list("DMSO1","DMSO2","DMSO3","SAM1","SAM2","SAM3"),
+                assembly="hg38",
+                treatment=c(1,1,1,0,0,0),
+                context="CpG",
+                mincov = 10,
+                dbtype = "tabix",
+                dbdir = "methylDB"
+                )

It ran for a like 2 hours and all I get is

Received list of locations.
creating directory methylDB ...
Error in file.exists(filepath) : invalid 'file' argument.

Should I not import the Dataset using From Text (base) and tab delineated option?
Am I missing hg38 assembly?
When I ran MethylDackel, I did extensive trimming with mbias. Could that have caused the problem? Should I lower mincov to 3 or something?
What does invalid file mean? Any help will be immensely appreciated. 

Thanks,

In Ki Cho

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Oct 23, 2021, 4:00:00 PM10/23/21
to methylkit_discussion
NVM guys. I answered my own question. I was stupid to import files into R. 
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