How to extract factor levels of coldata from deseq object?
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ariel ▴ 10
@ariel-16886
Last seen 11 months ago
United States

Suppose I have run deseq like this:

my_coldata$varA = factor(mycoldata$varA, levels=c('control', 'case')
my_coldata$varB = factor(mycoldata$varB, levels=c(0,1))

dds =  DESeqDataSetFromMatrix(
    countData=my_counts,
    colData=my_coldata,
    design=~varA + varB
  )

deseq_obj = DESeq(
    dds,
    test='Wald',
    fitType='mean'
  )

I can access the metadata with colData(deseq_obj) but it comes as a matrix with factor and level information wiped out. Is there a way to access this information?

Maybe a suggestion would be to switch to DataFrames since that is becoming ever more standard in the r-verse.

Thanks!

deseq2 levels factor colData • 746 views
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@mikelove
Last seen 1 day ago
United States

Check out the SummarizedExperiment package for details on how colData works. It is in fact a DataFrame.

You can just do dds$variable to print the variable and if it is a factor it will print the levels.

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I have a plotting routine to which I'm passing deseq_obj, and I was hoping I might get the levels in there. Well gollee, it IS a DataFrame. I had tried to extract the levels from the output of colData and thought I got an error and a matrix object. But as you said, it really is a DataFrame and has the levels. I can do colData(deseq_obj)$varA and get the levels.

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