| Age | Commit message (Collapse) | Author |
|---|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Delete the older test data that was only testing with `z` being a vector and
replace it with data that has `z` being a vector or matrix from data item to
data item.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/data_helpers.py: New function (`partition_by`)
* tests/unit/test_data_helpers.py: Tests for new function
Add a function that approximates Clojure's `partition-by` function, to help
with processing the data in a more functional way.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Fix a bug, caught when the function is called in a recursive form, with the
"z*" columns reducing for each cycle through the recursive form.
As it was, the last cycle through the recursive form would end up with a
DataFrame with the columns "x", "y", and "z0" rather than the columns "x",
"y", "z".
This commit handles that edge case to ensure that the column name is changed
from "z0" to simply "z".
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: Implement one path for the
`gn3.computations.partial_correlations.partial_correlation_recursive`
function.
* gn3/settings.py: Add a setting for how many decimal places to round to
* tests/unit/computations/test_partial_correlations.py: Update test to take
the number of decimal places into consideration
Implement a single path (where the z value is a vector and not a matrix) for
the `partial_correlation_recursive` function.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: new function (`build_data_frame`)
* tests/unit/computations/test_partial_correlations.py: Add tests for new
function
Add a new function to build a pandas DataFrame object from the provided
values:
- x: a vector of floats (represented with a tuple of floats)
- y: a vector of floats (represented with a tuple of floats)
- z: a vector OR matrix of floats (represented with a tuple of floats or a
tuple of tuples of floats)
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: new stub
functions (partial_correlation_matrix, partial_correlation_recursive)
*
tests/unit/computations/partial_correlations_test_data/pcor_mat_blackbox_test.csv:
blackbox sample data and results for variance-covariance matrix method
*
tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.csv:
blackbox sample data and results for recursive method
* tests/unit/computations/test_partial_correlations.py: Tests for new function
Provide some blackbox testing sample data for checking the operation of the
functions migrated from R.
|
|
* The missing dependency is causing the check pipeline to fail.
|
|
Issue:
* Stub out `determine_partials` which is a migration of
`web.webqtl.correlation.correlationFunction.determinePartialsByR` in GN1.
The function in GN1 has R code from line 188 to line 344. This will need to
be converted over to Python.
This function will also need tests.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Implement `compute_partial_correlations_fast` that is a partial migration of
`web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast` in
GN1.
This function will probably be reworked once the dependencies are fully
migrated.
It also needs tests to be added.
|
|
partial-correlations
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: New
function (good_dataset_samples_indexes).
* tests/unit/computations/test_partial_correlations.py: Tests for new
function (good_dataset_samples_indexes)
Get the indices of the selected samples. This is a partial migration of the
`web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast`
function in GN1.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/data_helpers.py: New function (parse_csv_line)
* tests/unit/test_data_helpers.py: Add tests for new function (parse_csv_line)
Add a function to parse a single line from a CSV file.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Add the `check_for_literature_info` and
`check_symbol_for_tissue_correlation` functions to check for the presence of
specific data.
|
|
* add biweight reimplementation with pingouin
* delete biweight scripts and tests
* add python-pingouin to guix file
* delete biweight paths
* mypy fix:pingouin mising imports
* pep8 formatting && pylint fixes
|
|
* Explicitly round the values to prevent issues with the type-checker
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: specify 10 decimal places
* tests/unit/computations/test_partial_correlations.py: update examples
Slight differences in python implementations, possibly hardware and
operating systems could cause the value of float (double) values to be
different in the less significant parts of the decimal places.
This commit limits the usable part of the decimals to the first 10 decimal
places for now.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/correlations.py: Remove the
`compare_tissue_correlation_absolute_values` function which is no longer
needed.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: Remove comments after updating
usage of the function at call point
* gn3/db/correlations.py: Complete the implementation of the
`build_temporary_tissue_correlations_table` function
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Complete the implementation of the `batch_computed_tissue_correlation`
function
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: new
function (`correlations_of_all_tissue_traits`).
* gn3/db/correlations.py: delete
function (`correlations_of_all_tissue_traits`).
Move the function to `gn3.computations.partial_correlations` module and
comment out the db-access code.
Rework it to receive, as arguments, the data it previously fetched from the
database, and add comments on future rework to get the function working
again.
|
|
partial-correlations
|
|
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: New function (tissue_correlation)
* tests/unit/test_partial_correlations.py ->
tests/unit/computations/test_partial_correlations.py: Move module. Implement
tests for new function
Migrate the `cal_tissue_corr` function embedded in the
`web.webqtl.correlation.correlationFunction.batchCalTissueCorr` function in
GN1 and implement tests to ensure it works correctly.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* The function `batch_computed_tissue_correlation` is a pure computations
function with no expressions accessing the database, as far as I can tell,
therefore, this commit moves the function over to the
gn3.computations.partial_correlations module that holds the pure computation
functions.
|
|
* Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Move the partial_correlations.py module to the gn3.computations module,
since it contains the computations for partial correlations.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Remove the if clauses to simplify the code flow: use a dictionary of queries
and select the appropriate query from the dictionary instead.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Stub out `batch_computed_tissue_correlation` function to be used in
implementing the function down the line.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Complete the implementation of the `correlations_of_all_tissue_traits`
function by providing a call to a non-implemented function.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Implement `fetch_gene_symbol_tissue_value_dict_for_trait` function which is
a migration of the
`web.webqtl.correlation.correlationFunction.getGeneSymbolTissueValueDictForTrait`
function in GeneNetwork1.
|
|
Partial correlations
|
|
* compare_tissue_correlation_absolute_values: New function. Complete. Used for
sorting of tissue correlation values
* fetch_symbol_value_pair_dict: New function. Complete. Maps gene symbols to
tissue expression data
* fetch_gene_symbol_tissue_value_dict: New function. Complete. Wrapper for
`gn3.db.correlations.fetch_symbol_value_pair_dict` function
* fetch_tissue_probeset_xref_info: New function. Complete. Retrieves the
Probeset XRef information for tissues from the database.
* correlations_of_all_tissue_traits: Stub. Dependencies not completed yet.
* build_temporary_tissue_correlations_table: Stub. Dependencies not completed
yet.
* fetch_tissue_correlations: New function. Incomplete. This function calls (a)
stub(s) function(s) which is/are under development still.
|
|
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/data_helpers.py: new function (partition_all)
* tests/unit/test_data_helpers.py: tests for function
`gn3.data_helpers.partition_all`
As part of migrating some functions that access the database, this commit
extracts generic processes that can be accomplished on data, and implements
the `partition_all` function, that is equivalent to Clojure's
`partition-all` function.
|
|
partial-correlations
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
