Add determine_nearest_neighbors to find nearest neighbors for each sample. Modify compute_stratified_metrics_filter to work with a comparison_sample_expr that specifies what samples to compare to for filtering, this works well with the output of determine_nearest_neighbor.
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…ples to compare to
klaricch
requested changes
Jan 12, 2023
gnomad/sample_qc/filtering.py
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| nbr=explode_nbrs_ht[hl.int64(explode_nbrs_ht.nearest_neighbor_idxs)].s | ||
| ) | ||
| explode_nbrs_ht = explode_nbrs_ht.group_by("s").aggregate( | ||
| nearest_neighbors=hl.agg.collect_as_set(explode_nbrs_ht.nbr) |
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does maintaining the order when collecting matter?
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Oh good point, if we ever want to map to the nearest_neighbor_dists array it needs to be in the same order
Co-authored-by: klaricch <[email protected]>
klaricch
reviewed
Jan 18, 2023
klaricch
approved these changes
Jan 23, 2023
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