Feature Area

Others

The Goal or Problem

In devel_pre_v4, quantData contains redundant stored data, and both data information readClassList and quantData are not completely documented. The goal is to tidy up the data structure for both readClassList & quantData for improved clarity and improved efficiency.

Also, quantData has to be something useful for the user, but not only used for repeated runs. We also plan to implement functions that generates unique count matrix and gene count matrix directly from quantData.

The Proposal & Example Usage (Optional)

# Example function to generate gene count matrix and unique count matrix from quantData
# Only quantData and (extended) annotations after transcript discovery is needed as input
generateUniqueCountMatrixFromQuantData(quantData,extendedAnno)
generateGeneCountMatrixFromQuantData(quantData,extendedAnno)

Checklist

• I searched existing issues to avoid duplicates.
• I described a concrete use case and success criteria.