How to extract top DEG and their sample values
0
Entering edit mode
ecg1g15 • 0
@ecg1g15-19970
Last seen 16 hours ago

I would like to know how to extract a dataframe containing the most Differentially Expressed Genes of my dataset but also the values for each sample, so I can use those for further analysis and visualisation plots.

After running this, I understand I see the genes with padj, Logfold basemean ETC

dds <- DESeq(dds)
res <- results(dds)
res


However, the output desired somwthing like this :

df

Genes            padj     Sample1     Sample2    Sample3     ...
Gene 1         0.0001      23423         42423        234234
Gene 2         0.001        23                 234            4234
Gene 3         0.01           2342             575          56756
...


Or just knowing how to extract the list of top DEG and their values across samples?

Thanks

DESeq2 RNASeq • 40 views
2
Entering edit mode
@u16406
Last seen 32 minutes ago
Republic of Ireland

Again, this is not related, specifically, to any issue with DESeq2, and would be more suited to a general bioinformatics or coding forum.

You can retrieve the 'normalised' counts via the DESeq2::counts() function (check the manual page for this function). If you want the transformed expression levels, then take a look at vst() and rlog(). These are all mentioned in the vignette. After that, you just need a few simple sub-setting commands in order to align the test statistics to these counts / expression levels.

Kevin