Entering edit mode
12 weeks ago
Gabriel
•
0
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.
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.