DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
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lu.la • 0
@lula-20604
Last seen 2.4 years ago
Paris

Hi,

I have a table of results from DEXSeq, but don't have the row data. I would like to plot some genes, using your plotDEXSeq function, but if I simply enter the dataframe I have, it returns an error

plotDEXSeq(DF, "Jak2", displayTranscripts=TRUE, legend=TRUE, cex.axis=1.2, cex=1.3, lwd=2 )

Error in plotDEXSeq(as.matrix(DF), "Jak2", displayTranscripts = TRUE, : is(object, "DEXSeqResults") | is(object, "DEXSeqDataSet") is not TRUE

I'd be happy to run DEXSeq from the information I have in the table.

dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design= ~ sample + exon + condition:exon, flattenedfile=flattenedFile )

I imagine there is a way as I have the counts. Something equivalent to DESeqDataSetFromMatrix. But I can't make it work. Here are the column contained in the table:

  • groupID featureID
    exonBaseMean
    dispersion
    stat
    pvalue
    padj
    genotype1
    genotype
    2
    log2foldgenotype2genotype1
    genomicData.seqnames
    genomicData.start
    genomicData.end genomicData.width
    genomicData.strand
    countData.Sample1genotype1
    countData.Sample
    3genotype1
    countData.Sample4genotype1
    countData.Sample
    7genotype1
    countData.Sample1genotype2
    countData.Sample
    3genotype2
    countData.Sample4genotype2
    countData.Sample
    7genotype2
    transcripts

row names are groupID:featureID

Is there a way to exploit this? Thank you for your help

DEXseq • 397 views
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Entering edit mode
Simon Anders ★ 3.7k
@simon-anders-3855
Last seen 2.4 years ago
Zentrum für Molekularbiologie, Universi…

The first argument in your call to "plotDEXSeq" should not be a data frame, but the DEXSeqDataSet object, i.e., "dxd". Try replacing "DF" with "dxd" in the call.

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Thank you for your answer. I might not have phrased my question clearly enough. What I meant is that I have a csv file with all the columns described. I have no idea how to import that as a DEXSeqDataSet. I imagine it means that I cannot make plot from this external file?

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