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-   -   EdgeR - how to convert DGELRT and other classes to .csv files (http://seqanswers.com/forums/showthread.php?t=66698)

lamartin 03-05-2016 02:12 PM

EdgeR - how to convert DGELRT and other classes to .csv files
 
Currently using edgeR to look at differential expression. I am struggling to take the edgeR values (specifically DGELRT-class produced after the QL F-test) and convert them to .csv files.

I am frustrated with edgeR because it does not seem there is an easy way to do this. The edgeR package has excellent documentation, I cannot find help for extract the information generated.

It is not included in the examples in the user manual. Subsetting, suggested in user manual (https://bioconductor.org/packages/re.../man/edgeR.pdf) simply makes another DGELRT class. I cannot find the Extract option in the baseline package.

Any thoughts on how to take a DGELRT value and make it a data object in R (to be written as a .csv file)?

lamartin 03-05-2016 02:42 PM

Answer provided by Aaron Lun on bioconductor:
out <- topTags(results, n=Inf)
write.csv(out, file="blah.csv")


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