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Add generic constraint functions: oe_aggregation_expr(), compute_pli(), oe_confidence_interval(), calculate_raw_z_score(), calculate_raw_z_score_sd() #505

Merged
merged 44 commits into from
Apr 14, 2023
Merged

Add generic constraint functions: oe_aggregation_expr(), compute_pli(), oe_confidence_interval(), calculate_raw_z_score(), calculate_raw_z_score_sd() #505

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4897b17
add draft
Nov 2, 2022
88b1941
add draft
Nov 2, 2022
ebc0e7e
add comments
Nov 9, 2022
c9116b7
black reformat
Nov 9, 2022
dffd326
merge main
Nov 9, 2022
588f818
Apply suggestions from code review
averywpx Nov 29, 2022
8966efb
fix change requests
Dec 1, 2022
06bec20
small fix
Dec 1, 2022
59eb457
add comments
Dec 1, 2022
0c9148e
add filter for compute_oe_per_transcript
Dec 1, 2022
ec371a5
Apply suggestions from code review
jkgoodrich Mar 3, 2023
f827d30
Merge branch 'main' of https://github.com/broadinstitute/gnomad_metho…
jkgoodrich Mar 3, 2023
5a64d72
Modifications to make most of the functions return expressions
jkgoodrich Mar 7, 2023
db5f159
Fixes during testing
jkgoodrich Mar 14, 2023
65581f0
Add docstrings
jkgoodrich Mar 14, 2023
4c98b60
Remove unneeded f-strings
jkgoodrich Mar 17, 2023
8f593bc
Apply suggestions from code review
jkgoodrich Mar 20, 2023
4649470
Merge branch 'constraint_finalize_datasets' of https://github.com/bro…
jkgoodrich Mar 20, 2023
33d0b60
Fix docstring for calculate_raw_z_score
jkgoodrich Mar 20, 2023
6badab5
Update gnomad/utils/constraint.py
jkgoodrich Mar 21, 2023
65f3f8c
Z-score -> z-score, delete unused function, and add ht to parameters
jkgoodrich Mar 21, 2023
911123c
small edit
klaricch Mar 23, 2023
5a44ea5
Changes during PR review
jkgoodrich Mar 28, 2023
a31ee84
Change `calculate_z_score` to `calculate_raw_z_score_sd` and modify i…
jkgoodrich Apr 2, 2023
27909d7
Use `add_filters_expr` for constraint filters and add `no_var_expr` p…
jkgoodrich Apr 2, 2023
a9e55b9
Fix `oe_confidence_interval` docstring
jkgoodrich Apr 2, 2023
bf476a0
Set dpois to missing if `exp_expr > 0`
jkgoodrich Apr 3, 2023
1dbbd19
Change constraint flags to include flag_prefix and remove no_variants…
jkgoodrich Apr 4, 2023
6b39fbb
Change expected_values default so it's not mutable.
jkgoodrich Apr 4, 2023
bdfdf38
Small docstring change
jkgoodrich Apr 4, 2023
a8c6719
Fix NaN returned for oe
jkgoodrich Apr 4, 2023
c2f792f
pli exclude exp 0
jkgoodrich Apr 4, 2023
b540b8f
return correct missing type for oe_aggregation_expr
jkgoodrich Apr 4, 2023
6ea9f21
constraint flags prefix -> postfix
jkgoodrich Apr 4, 2023
e29fddc
Remove redundancy with dpois_expr
jkgoodrich Apr 4, 2023
aee69bd
Use divide_null in calculate_raw_z_score
jkgoodrich Apr 4, 2023
635f98c
Fix types
jkgoodrich Apr 13, 2023
bcfee5c
Merge branch 'main' of https://github.com/broadinstitute/gnomad_metho…
jkgoodrich Apr 13, 2023
b0b12ad
Merge branch 'main' of https://github.com/broadinstitute/gnomad_metho…
jkgoodrich Apr 13, 2023
3019cc3
Merge branch 'constraint_finalize_datasets' of https://github.com/bro…
jkgoodrich Apr 13, 2023
b147e98
Small docstring change
jkgoodrich Apr 13, 2023
65a698f
Docstring fixes
jkgoodrich Apr 13, 2023
dfe085a
change `calculate_raw_z_score_sd` to have `mirror_neg_raw_z` instead …
jkgoodrich Apr 14, 2023
889f62a
Merge pull request #526 from broadinstitute/constraint_finalize_datas…
jkgoodrich Apr 14, 2023
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