Add generic constraint functions: oe_aggregation_expr(), compute_pli(), oe_confidence_interval(), calculate_raw_z_score(), calculate_raw_z_score_sd()
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klaricch
requested changes
Nov 22, 2022
Co-authored-by: klaricch <kristen@broadinstitute.org>
averywpx
commented
Dec 1, 2022
klaricch
requested changes
Mar 1, 2023
gnomad/utils/constraint.py
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| :param prefix: Prefix of upper and lower bounds, defaults to 'oe'. | ||
| :param alpha: The significance level used to compute the confidence interval. | ||
| Default is 0.05. | ||
| :param select_only_ci_metrics: Whether to return only upper and lower bounds |
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will we ever need this to be false or can we just remove this?
gnomad/utils/constraint.py
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| :param ht: Input Table with pLoF variants, missense variants, or synonymous | ||
| variants. | ||
| :param annotation_name: Annotation name used for constraint metrics to distinguish |
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maybe should provide some examples here
jkgoodrich
reviewed
Mar 3, 2023
gnomad/utils/constraint.py
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Comment on lines
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| over a range of lambda (`lamb` in `dpois`) values, which are given by the expected | ||
| number of variants times a varying parameter ranging between 0 and 2. The |
gnomad/utils/constraint.py
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| """ | ||
| ht = ht.annotate(_obs=obs, _exp=exp) | ||
| # Set up range between 0 and 2. | ||
| oe_ht = ht.annotate(_range=hl.range(0, 2000).map(lambda x: hl.float64(x) / 1000)) |
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Should these be parameters, why 1000?
gnomad/utils/constraint.py
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| oe_ht = oe_ht.transmute( | ||
| **{ | ||
| f"{prefix}_lower": hl.if_else( | ||
| oe_ht._obs > 0, oe_ht._range[oe_ht._lower_idx], 0 |
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Add to docstring that we cut this off
Co-authored-by: klaricch <kristen@broadinstitute.org>
… into constraint_finalize_datasets � Conflicts: � gnomad/utils/constraint.py
klaricch
reviewed
Mar 13, 2023
klaricch
requested changes
Mar 20, 2023
Co-authored-by: klaricch <kristen@broadinstitute.org>
…t to only return the std dev of the raw z-score
jkgoodrich
requested changes
Apr 4, 2023
… into constraint_finalize_datasets_jkg
… into constraint_finalize_datasets
…adinstitute/gnomad_methods into constraint_finalize_datasets_jkg
…of `neg_raw_z_only` and `both`
…ets_jkg Suggested changes to the Add generic constraint functions: compute_oe_per_transcript(), compute_all_pLI_scores(), pLI(), oe_confidence_interval(), calculate_z(), calculate_z_scores() PR
jkgoodrich
changed the title
compute_oe_per_transcript(), compute_all_pLI_scores(), pLI(), oe_confidence_interval(), calculate_z(), calculate_z_scores() oe_aggregation_expr(), compute_pli(), oe_confidence_interval(), calculate_raw_z_score(), calculate_raw_z_score_sd()
klaricch
approved these changes
Apr 14, 2023
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Add generic constraint functions used to compute constraint metrics.