Rsubread: change in behavior when accepting mixed paired end and single end files

Question

[barrel0luck]

I'd a question regarding a recent change in the Rsubread package. I routinely deal with mixed paired end and single end data.

The Rsubread function featureCounts had a isPairedEnd argument that used to accept a logical vector containing information of which files are paired end or not.

That seems to no longer work and Rsubread only takes the first logical and applies that to all files.

As a result, many of my scripts have stopped working.

Does anyone know if this is a bug or whether this is expected behaviour?

I've written to one of the maintainers, but I was wondering if anyone else has faced issues and knows what to do about it?

[ATpoint]

You should post this over at support.bioconductor.org since this is a Bioconductor package.

[barrel0luck]

Thanks, I'll try there as well. I did see some posts on Rsubread here as well.