Question: edgeR - how to convert DGELRT and other classes to .csv files
0
gravatar for cellbiologyhelp
3.2 years ago by
cellbiologyhelp0 wrote:

I am using edgeR to look for differential expression.  I am struggling to export data generated in edgeR (specifically DGELRT-class information, produced after the QL F-test) and convert it to .csv file.

The edgeR package has excellent documentation for working within the package.  My only frustrating is exporting data, it does not seem there is an easy way to get the results of the QL F-test.  I do not see this addressed in the examples contained the user guide.  The user manual addresses subsetting, but this simply makes another DGELRT class. I cannot find the Extract option in the baseline package.  I am unclear of what the “baseline package” is, as there is edgeR and edge in Bioconductor.

Can anyone help me or provide me with resources/guidance to take a DGELRT value and make it a data object in R (to be written as a .csv file)?

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by cellbiologyhelp0
Answer: edgeR - how to convert DGELRT and other classes to .csv files
3
gravatar for Aaron Lun
3.2 years ago by
Aaron Lun23k
Cambridge, United Kingdom
Aaron Lun23k wrote:

Try the topTags function. For example, if you have a DGELRT object named results:

out <- topTags(results, n=Inf)
write.csv(out, file="blah.csv")

Check out the man pages to get specific options, e.g., if you don't want sorting by p-value.

ADD COMMENTlink written 3.2 years ago by Aaron Lun23k
Answer: edgeR - how to convert DGELRT and other classes to .csv files
0
gravatar for cellbiologyhelp
3.2 years ago by
cellbiologyhelp0 wrote:

This is exactly what I wanted to do!!! Thank you for prompt response!!

ADD COMMENTlink written 3.2 years ago by cellbiologyhelp0
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