fix: score HPA genes over the cell types they were measured in - #680
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The HPA cell-type reduction built a sparse GENESxCELLTYPES score matrix and reduced over the full row. Sparse structural zeros are numeric zeros, and 0 sits between 'Low' (10) and 'Not detected' (-8), so under the default 'max' a gene not detected in one of two cell types scored 0 rather than -8. Measured: 0. Since hpaScores override arrayScores and removeLowScoreGenes prunes only below zero, such a gene was then never pruned. 'average' had the matching defect, dividing by the number of cell types rather than the number of measurements. Both now reduce over the measurements that exist, which is what the arrayData branch above already does. Adds a test for a gene measured in one of two cell types.
Function test results241 tests 219 ✅ 1m 2s ⏱️ Results for commit 7f16635. |
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Main improvements in this PR:
scoreComplexModelscored an unmeasured cell type as 0, and 0 outranks 'Not detected' (-8). A gene not detected in one of two cell types therefore scored 0 under the default'max', and was never pruned byremoveLowScoreGenes, which only prunes below zero.'average'likewise divided by the number of cell types rather than the number of measurements. Both now reduce over the measurements that exist.tINIT.mfor a gene measured in one of two cell types.Instructions on merging this PR:
develop3as target branch, and will be resolved with a squash-merge.