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* remove extra iteration that is unnecessary
* remove unnecessary variables
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* gn3/computations/correlations.py: rename function
* mypy.ini: deactivate mypy error about missing imports
* tests/integration/test_correlation.py: mock correct function
* tests/unit/computations/test_correlation.py: test correct function
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* To help speed up the processing of the correlations, convert the
`compute_all_sample_correlation` function to use the multiprocessing module.
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The `fix_strains` function works on the trait data, not the basic trait
info. This commit fixes the arguments passed to the function, and also some
bugs in the function.
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* Add a new script to compute the partial correlations against:
- a select list of traits, or
- an entire dataset
depending on the specified subcommand. This new script is meant to supercede
the `scripts/partial_correlations.py` script.
* Fix the check for errors
* Reorganise the order of arguments for the
`partial_correlations_with_target_traits` function: move the `method`
argument before the `target_trait_names` argument so that the common
arguments in the partial correlation computation functions share the same
order.
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Rework the code to process the traits in a single iteration to improve
performance.
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Return generator objects rather than pre-computed tuples to reduce the number
of iterations needed to process the data, and thus improve the performance of
the system somewhat.
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Enable the endpoint to actually compute partial correlations with selected
target traits rather than against an entire dataset.
Fix some issues caused by recent refactor that broke pcorrs against a dataset
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Compute partial correlations against a selection of traits rather than against
an entire dataset.
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* Extract the common error checking code into a separate function
* Rename the function to make its use clearer
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Remove an unnecessary looping construct to help with speeding up the partial
correlations somewhat.
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* Remove a module that is no longer in use
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See: <https://ci.genenetwork.org/jobs/genenetwork3-pylint/126>
* gn3/computations/rqtl.py: Run `black gn3/computations/rqtl.py`. Also,
manually fix other pylint issues.
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position in pair-scan results + return only the sorted top 500 results
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it's needed to store the proximal/distal markers for each position
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Dict and List respectively used for the pair scan figure and the table showing the results
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in pairscan results + renamed process_rqtl_output to process_rqtl_mapping to distinguish between that and pairscan
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* compute zscore function
* test case for computing zscore
* function to compute pca
* generate scree plot data
* generate new pca trait data from zscores and eigen_vec
* remove redundant functions
* generate factor loading table data
* generate pca temp dataset dict
* variable naming and error fixes
* unit test for processing factor loadings
* minor fixes for generating temp pca dataset
* pass datetime as argument to generate_pca temp dataset function
* add unittest for caching pca datasets
* cache temp datasets
* ignore missing imports for sklearn
* mypy fixes
* pylint fixes
* refactor tests for pca
* remove ununsed imports
* fix for generating pca traits vals
* mypy and code refactoring
* pep8 formatting and add docstrings
* remove comments /pep8 formatting
* sort eigen vectors based on eigen values
* minor fix for zscores
* fix for rounding variance ratios
* refactor tests
* rename module to pca
* rename datasets to traits
* fix failing tests
* fix caching function
* fixes return x and y coordinates for scree plot
* expand exception scope
* fix for deprecated numpy.matrix function
* fix for failing tests
* pep8 fixes
* remove comments
* fix merge conflict
* pylint fixes
* rename module name to test_pca
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