Genes of Interest in a Multi-Tissue Analysis
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.
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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.