Description of feature request
When thresholding mitochondrial content, scater::isOutlier() is used with the argument type = "both". This tests both tails of the distribution of mitochondrial content for outliers. While this makes sense for single cell, for single nucleus we should only test the higher end of the distribution (see OSCA Advanced, Section 11.2).
Description of solution
Permit users to input type in scater::isOutlier() when used for quality control of mitochondrial content in annotate_sce_cells(). For backwards compatibility, default argument can be set to "both".
Description of feature request
When thresholding mitochondrial content,
scater::isOutlier()is used with the argumenttype = "both". This tests both tails of the distribution of mitochondrial content for outliers. While this makes sense for single cell, for single nucleus we should only test the higher end of the distribution (see OSCA Advanced, Section 11.2).Description of solution
Permit users to input
typeinscater::isOutlier()when used for quality control of mitochondrial content inannotate_sce_cells(). For backwards compatibility, default argument can be set to "both".