Genes of Interest in a Multi-Tissue Analysis

Question

[Gabriel]

I am conducting an analysis in DESeq2 of different parts of a plant (leaf, stem, root,..) in replicates. I have created a DESeqDataSet (dds) of the whole gene count table and am using VST-transformed counts to profile each sample. Now, I want to select only the genes from my list and view the profile of each sample for this subset of genes of interest.

Here is my code:

ddsAll <- DESeqDataSetFromMatrix(countData = round(tissue_quant),
                              colData = coldata,
                              design = ~ tissue + 0)   

ddsAll <- DESeq(ddsAll)

vsd <- vst(ddsAll, blind = FALSE, nsub = sum( rowMeans( counts(ddsAll, normalized=TRUE)) > 20 ))

It's possible create an subset object from vsd with only my genes of interest?

Thank you for your help.

[allingt]

The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applicable for its subsetting may also be usable for vst() output.