Mapping DESeq2 output back to chromosomal positions
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rbronste ▴ 60
@rbronste-12189
Last seen 22 months ago

So I output a matrix from DiffBind as my input into DESeq2, with the chromosome positions being removed from the count matrix, just leaving the first column key as a reference followed by the counts in all the replicates in the matrix:

dds<-DESeqDataSetFromMatrix(countData = countData,
                            colData = colData,
                            design =  ~ sex + treatment)

Following this I ran DESeq2 and have output the results as follows:

write.csv(as.data.frame(results), file="results.csv")

Now this of course is a limited list by LFC and adjusted p-val so I was wondering how I can remap this list to the original matrix output from DiffBind so I can recover the chromosome positions since this contains only the key. 

Thanks!

 

deseq2 deseq diffbind differential binding analysis • 640 views
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I guess another way to look at is how to from the following results recover the associated countData?

head(results)
log2 fold change (MLE): +1,-0.333333333333333,-0.333333333333333,-0.333333333333333 
Wald test p-value: +1,-0.333333333333333,-0.333333333333333,-0.333333333333333 
DataFrame with 6 rows and 6 columns
        baseMean log2FoldChange     lfcSE      stat    pvalue      padj
       <numeric>      <numeric> <numeric> <numeric> <numeric> <numeric>
440385  24.01924      -2.625855  1.659993 0.0000000        NA        NA
440386  30.58690       4.390651  1.499186 1.5946323        NA        NA
440387  32.86232       2.876218  1.407257 0.6226421 0.2667599         1
440388  19.38288      -1.482686  1.485418 0.0000000 0.9904758         1
440389  80.59038       1.277523  1.458940 0.0000000 0.6897729         1
440390  41.60001       0.122999  1.434733 0.0000000 0.9046071         1
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@mikelove
Last seen 5 hours ago
United States

You can match by the rownames, right? Here you would just use base R functionality, e.g. ordering by a character vector of rownames with square brackets or using the match() function.

Note that DESeqDataSet is actually built on RangedSummarizedExperiment objects, and so results() can output *ranges* in this case, see ?results. This would be my preferred option, to give DESeq2 ranged data to begin with, and then the package will keep track of this for you.

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I guess another way I considered doing it is by adding the (CHR, START, STOP) columns as metadata to the: 

DESeqDataSetFromMatrix

As they would be there initially from DiffBind if I did not strip them out. This would leave them in the results if I understand correctly? 

Is there a good way to go about this given the info above? Thanks!

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I’d recommend making a RangedSummarizedExperiment object (it’s the same amount of work as what you are suggesting) then use DESeqDataSet(rse, design). Then everything will “just work”, and you can get a ranged results table.

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Thanks for the advice! 

I think the following (from DiffBind) should do the job of outputting the RangedSummarizedExperiment object that I can use in DESeq2.

dba.peakset
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