How to subset the output of tximport in DE analysis using DEseq2

Question

[tianshenbio]

I have a dataset of 32 samples quantified using salmon. I used tximport to import the data:

txi=tximport(c(a vector of file names),type="salmon",tx2gene=tx2gene)

I have created the colData and used DESeqDataSetFromTximport to construct the Deseq2 data set:

dds <- DESeqDataSetFromTximport(txi = txi,colData = col_data,design = ~ Form)

In this case, all 32 samples are used, now I only want to use a subset of txi by choosing specific samples. Is there a way to subset my current txi rather than constructing a new txi using only the samples that I want?

[dew]

Does this means after the subset, you should reset the design to the situation of the subset? Thanks!

[ATpoint]

If the filter changed the design (like removing an entire group), then probably yes.

Answer 1

[ATpoint]

The DESeq2 object is basically a SummarizedExperiment so you can subset this prior to running DESeq using standard operations such as dds_use <- dds[,c(columns_to_keep] where columns_to_keep is a numeric vector with the columns (samples) you want to use.

[tianshenbio]

That is clear! Thank you for your explanation.