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There are situations when blocking can lead to non-full rank matrices in DESeq2 unless the data are subset to specific samples (e.g. when some samples are paired and these need to be compared, but there are other samples without pairing).
This request is for a feature to subset to samples for specific contrasts.
This could potentially be done by providing a single boolean option for a contrast to subset the data to only samples involved in the contrast (which may be otherwise useful), or providing a reference to another column in the sample sheet that specifies which samples to include.
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enhancementNew feature or requestNew feature or request