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Aug 31, 2020
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Add missing API docs to Sphinx #214

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25 changes: 23 additions & 2 deletions docs/api.rst
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Expand Up @@ -6,11 +6,32 @@ API reference

This page provides an auto-generated summary of sgkits's API.

Top-level functions
===================
Creating a dataset
==================

.. autosummary::
:toctree: generated/

create_genotype_call_dataset
create_genotype_dosage_dataset
read_vcfzarr

Methods
=======

.. autosummary::
:toctree: generated/

count_call_alleles
count_variant_alleles
gwas_linear_regression
hardy_weinberg_test
regenie

Utilities
=========

.. autosummary::
:toctree: generated/

display_genotypes
2 changes: 1 addition & 1 deletion sgkit/api.py
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Expand Up @@ -93,7 +93,7 @@ def create_genotype_dosage_dataset(
call_genotype_probability: Any,
variant_id: Any = None,
) -> xr.Dataset:
"""Create a dataset of genotype calls.
"""Create a dataset of genotype dosages.

Parameters
----------
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7 changes: 4 additions & 3 deletions sgkit/stats/hwe.py
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Expand Up @@ -145,7 +145,7 @@ def hardy_weinberg_test(
Dataset
Dataset containing (N = num variants):
variant_hwe_p_value : (N,) ArrayLike
P values from HWE test for each variant as float in [0, 1].
P values from HWE test for each variant as float in [0, 1].

References
----------
Expand All @@ -156,8 +156,9 @@ def hardy_weinberg_test(
Raises
------
NotImplementedError
* If ploidy of provided dataset != 2
* If maximum number of alleles in provided dataset != 2
If ploidy of provided dataset != 2
NotImplementedError
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I had originally been breaking multiple causes of the same error out like this but @ravwojdyla suggested collapsing them in a past PR. @ravwojdyla did you have a reason for that?

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Sphinx doesn't render the bullets correctly, which is why I changed this.

If maximum number of alleles in provided dataset != 2
"""
if ds.dims["ploidy"] != 2:
raise NotImplementedError("HWE test only implemented for diploid genotypes")
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31 changes: 16 additions & 15 deletions sgkit/stats/regenie.py
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Expand Up @@ -736,7 +736,7 @@ def regenie(
) -> Dataset:
"""Regenie trait transformation.

[REGENIE](https://github.com/rgcgithub/regenie) is a whole-genome
`REGENIE <https://github.com/rgcgithub/regenie>`_ is a whole-genome
regression technique that produces trait estimates for association
tests. These estimates are subtracted from trait values and
sampling statistics (p-values, standard errors, etc.) are evaluated
Expand Down Expand Up @@ -790,14 +790,20 @@ def regenie(
Dataset
A dataset containing the following variables:
- `base_prediction` (blocks, alphas, samples, outcomes): Stage 1
predictions from ridge regression reduction .
predictions from ridge regression reduction .
- `meta_prediction` (samples, outcomes): Stage 2 predictions from
the best meta estimator trained on the out-of-sample Stage 1
predictions.
the best meta estimator trained on the out-of-sample Stage 1
predictions.
- `loco_prediction` (contigs, samples, outcomes): LOCO predictions
resulting from Stage 2 predictions ignoring effects for variant
blocks on held out contigs. This will be absent if the
data provided does not contain at least 2 contigs.
resulting from Stage 2 predictions ignoring effects for variant
blocks on held out contigs. This will be absent if the
data provided does not contain at least 2 contigs.

Raises
------
ValueError
If dosage, covariates, and trait arrays do not have the same number
of samples.

Examples
--------
Expand All @@ -824,15 +830,10 @@ def regenie(
References
----------
[1] - Mbatchou, J., L. Barnard, J. Backman, and A. Marcketta. 2020.
“Computationally Efficient Whole Genome Regression for Quantitative and Binary
Traits.” bioRxiv. https://www.biorxiv.org/content/10.1101/2020.06.19.162354v2.abstract.
[2] - https://glow.readthedocs.io/en/latest/tertiary/whole-genome-regression.html
“Computationally Efficient Whole Genome Regression for Quantitative and Binary
Traits.” bioRxiv. https://www.biorxiv.org/content/10.1101/2020.06.19.162354v2.abstract.

Raises
------
ValueError
If dosage, covariates, and trait arrays do not have the same number
of samples.
[2] - https://glow.readthedocs.io/en/latest/tertiary/whole-genome-regression.html
"""
if isinstance(covariates, str):
covariates = [covariates]
Expand Down