This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to subset the output of tximport in DE analysis using DEseq2

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?

deseq2 tximport rna-seq r
• 4,415 views • link
updated by ATpoint ATpoint • written by tianshenbio tianshenbio

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

• 0 views • link
written by dew • dew

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

• 0 views • link
written by ATpoint ATpoint

1 answer

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.

• 0 views • link
written by ATpoint ATpoint

That is clear! Thank you for your explanation.

• 0 views • link
written by tianshenbio tianshenbio

Log in to answer this question.

More posts like this