Mosaic data integration is improved by capturing features that do not overlap between datasets
We used the PBMC 10x Multiome data to evaluate StabMap under the situation of multi-hop mosaic data integration. We downloaded and processed the data as described in the subsection above, with the exception that promoter peaks corresponding to specific genes were not matched to the associated genes. This resulted in a complete lack of overlap between features between the RNA and chromatin modalities.
To perform the simulation, we randomly allocated each cell into one of three classes: RNA only, chromatin only and Multiome, with varying relative proportions of cells associated with the Multiome class. Cells within the RNA class had their chromatin information ignored, and cells within the chromatin class had their RNA information ignored, while cells within the Multiome class were left unchanged.
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