Documentation for WGR #235
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Add Leland's demo notebook
…or WGR (#2) * blocks Signed-off-by: kianfar77 <[email protected]> * test vcf Signed-off-by: kianfar77 <[email protected]> * transformer Signed-off-by: kianfar77 <[email protected]> * remove extra Signed-off-by: kianfar77 <[email protected]> * refactor and conform with ridge namings Signed-off-by: kianfar77 <[email protected]> * test Signed-off-by: kianfar77 <[email protected]> * test files Signed-off-by: kianfar77 <[email protected]> * remove extra file Signed-off-by: kianfar77 <[email protected]> * sort_key Signed-off-by: kianfar77 <[email protected]>
* feat: ridge models for wgr added Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> * Doc strings added for levels/functions.py Some typos fixed in ridge_model.py Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> * ridge_model and RidgeReducer unit tests added Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> * RidgeRegression unit tests added test data README added ridge_udfs.py docstrings added Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> * Changes made to accessing the sample ID map and more docstrings The map_normal_eqn and score_models functions previously expected the sample IDs for a given sample block to be found in the Pandas DataFrame, which mean we had to join them on before the .groupBy().apply(). These functions now expect the sample block to sample IDs mapping to be provided separately as a dict, so that the join is no longer required. RidgeReducer and RidgeRegression APIs remain unchanged. docstrings have been added for RidgeReducer and RidgeRegression classes. Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> * Refactored object names and comments to reflect new terminology Where 'block' was previously used to refer to the set of columns in a block, we now use 'header_block' Where 'group' was previously used to refer to the set of samples in a block, we now use 'sample_block' Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]>
* WIP Signed-off-by: Karen Feng <[email protected]> * existing tests pass Signed-off-by: Karen Feng <[email protected]> * rename file Signed-off-by: Karen Feng <[email protected]> * Add compat test Signed-off-by: Karen Feng <[email protected]> * scalafmt Signed-off-by: Karen Feng <[email protected]> * collect minimal columns Signed-off-by: Karen Feng <[email protected]> * address comments Signed-off-by: Karen Feng <[email protected]> * Test fixup Signed-off-by: Karen Feng <[email protected]> * Spark 3 needs more recent PyArrow, reduce mem consumption by removing unnecessary caching Signed-off-by: Karen Feng <[email protected]> * PyArrow 0.15.1 only with PySpark 3 Signed-off-by: Karen Feng <[email protected]> * Don't use toPandas() Signed-off-by: Karen Feng <[email protected]> * Upgrade pyarrow Signed-off-by: Karen Feng <[email protected]> * Only register once Signed-off-by: Karen Feng <[email protected]> * Minimize memory usage Signed-off-by: Karen Feng <[email protected]> * Select before head Signed-off-by: Karen Feng <[email protected]> * set up/tear down Signed-off-by: Karen Feng <[email protected]> * Try limiting pyspark memory Signed-off-by: Karen Feng <[email protected]> * No teardown Signed-off-by: Karen Feng <[email protected]> * Extend timeout Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
* WIP Signed-off-by: Karen Feng <[email protected]> * existing tests pass Signed-off-by: Karen Feng <[email protected]> * rename file Signed-off-by: Karen Feng <[email protected]> * Add compat test Signed-off-by: Karen Feng <[email protected]> * scalafmt Signed-off-by: Karen Feng <[email protected]> * collect minimal columns Signed-off-by: Karen Feng <[email protected]> * start changing for readability * use input label ordering * rename create_row_indexer * undo column sort * change reduce Signed-off-by: Henry D <[email protected]> * further simplify reduce * sorted alpha names * remove ordering * comments Signed-off-by: Henry D <[email protected]> * Set arrow env var in build Signed-off-by: Henry D <[email protected]> * faster sort * add test file * undo test data change * >= * formatting * empty Co-authored-by: Karen Feng <[email protected]>
* yapf Signed-off-by: Karen Feng <[email protected]> * yapf transform Signed-off-by: Karen Feng <[email protected]> * Set driver memory Signed-off-by: Karen Feng <[email protected]> * Try changing spark mem Signed-off-by: Karen Feng <[email protected]> * match java tests Signed-off-by: Karen Feng <[email protected]> * whoops Signed-off-by: Karen Feng <[email protected]> * remove driver memory flag Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: kianfar77 <[email protected]>
* cleanup Signed-off-by: Karen Feng <[email protected]> * whoops Signed-off-by: Karen Feng <[email protected]> * cleanup Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
* WIP Signed-off-by: Karen Feng <[email protected]> * WIP Signed-off-by: Karen Feng <[email protected]> * WIP Signed-off-by: Karen Feng <[email protected]> * WIP Signed-off-by: Karen Feng <[email protected]> * WIP Signed-off-by: Karen Feng <[email protected]> * whoops Signed-off-by: Karen Feng <[email protected]> * tests Signed-off-by: Karen Feng <[email protected]> * simplify tests Signed-off-by: Karen Feng <[email protected]> * WIP Signed-off-by: Karen Feng <[email protected]> * yapf Signed-off-by: Karen Feng <[email protected]> * index map compat Signed-off-by: Karen Feng <[email protected]> * Add docs Signed-off-by: Karen Feng <[email protected]> * Add more tests Signed-off-by: Karen Feng <[email protected]> * pass args as ints Signed-off-by: Karen Feng <[email protected]> * Don't roll our own splitter Signed-off-by: Karen Feng <[email protected]> * rename sample_index to sample_blocks Signed-off-by: Karen Feng <[email protected]>
* Add type-checking to APIs Signed-off-by: Karen Feng <[email protected]> * Check valid alphas Signed-off-by: Karen Feng <[email protected]> * check 0 sig Signed-off-by: Karen Feng <[email protected]> * Add to install_requires list Signed-off-by: Karen Feng <[email protected]> * cleanup comments Signed-off-by: Karen Feng <[email protected]>
* Added necessary modifications to accomodate covariates in model fitting. The initial formulation of the WGR model assumed a form y ~ Xb, however in general we would like to use a model of the form y ~ Ca + Xb, where C is some matrix of covariates that are separate from the genomic features X. This PR makes numerous changes to accomodate covariate matrix C. Adding covariates required the following breaking changes to the APIs: * indexdf is now a required argument for RidgeReducer.transform() and RidgeRegression.transform(): * RidgeReducer.transform(blockdf, labeldf, modeldf) -> RidgeReducer.transform(blockdf, labeldf, indexdf, modeldf) * RidgeRegression.transform(blockdf, labeldf, model, cvdf) -> RidgeRegression.transform(blockdf, labeldf, indexdf, model, cvdf) Additionally, the function signatures for the fit and transform methods of RidgeReducer and RidgeRegression have all been updated to accomodate an optional covariate DataFrame as the final argument. Two new tests have been added to test_ridge_regression.py to test run modes with covariates: * test_ridge_reducer_transform_with_cov * test_two_level_regression_with_cov Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> * Cleaned up one unnecessary Pandas import Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> * Small changes for clarity and consistence with the rest of the code. Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> * Forgot one usage of coalesce Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> * Added a couple of comments to explain logic and replaced usages of .values with .array Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> * Fixed one instance of the change .values -> .array where it was made in error. Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> * Typo in test_ridge_regression.py. Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> * Style auto-updates with yapfAll Signed-off-by: Leland Barnard ([email protected]) Signed-off-by: Leland Barnard <[email protected]> Co-authored-by: Leland Barnard <[email protected]> Co-authored-by: Karen Feng <[email protected]>
* WIP Signed-off-by: Karen Feng <[email protected]> * Clean up tests Signed-off-by: Karen Feng <[email protected]> * WIP Signed-off-by: Karen Feng <[email protected]> * Order to match labeldf Signed-off-by: Karen Feng <[email protected]> * Check we tie-break Signed-off-by: Karen Feng <[email protected]> * cleanup Signed-off-by: Karen Feng <[email protected]> * tests Signed-off-by: Karen Feng <[email protected]> * test var name Signed-off-by: Karen Feng <[email protected]> * clean up tests Signed-off-by: Karen Feng <[email protected]> * Clean up docs Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
…wgr-docs Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
* Rename levels to wgr Signed-off-by: Karen Feng <[email protected]> * rename test files Signed-off-by: Karen Feng <[email protected]>
* headers * executable * fix template rendering * yapf
Signed-off-by: Karen Feng <[email protected]>
…wgr-docs Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
…-docs Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Codecov Report
@@ Coverage Diff @@
## master #235 +/- ##
=======================================
Coverage 93.75% 93.75%
=======================================
Files 90 90
Lines 4339 4339
Branches 406 406
=======================================
Hits 4068 4068
Misses 271 271 Continue to review full report at Codecov.
|
…-docs Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
|
|
||
| The genotype data may be read from any variant datasource supported by Glow, such as VCF, BGEN or PLINK. The DataFrame | ||
| must also include a column ``values`` containing a numeric representation of each genotype. The genotypic values may | ||
| not be missing, or equal for every sample in a variant. |
There was a problem hiding this comment.
what does equal mean here? All homozygous reference?
There was a problem hiding this comment.
Mathematically, we're trying to filter out variants for which all samples have the same calls and therefore values has a variance/stddev of 0 (eg.
all hom ref, all hom-alt, or even all het). I'm not sure what the best way to phrase this is.
| - Split multiallelic variants with the ``split_multiallelics`` transformer. | ||
| - Calculate the number of alternate alleles for biallelic variants with ``glow.genotype_states``. | ||
| - Replace any missing values with the mean of the non-missing values using ``glow.mean_substitute``. | ||
| - Filter out all homozygous SNPs. |
There was a problem hiding this comment.
Filter out all SNPs that contain zero non-reference alleles
| The fields in the model DataFrame are: | ||
|
|
||
| - ``header_block``: An ID assigned to the block x0 corresponding to the coefficients in this row. | ||
| - ``sample_block``: An ID assigned to the block x0 corresponding to the coefficients in this row. |
There was a problem hiding this comment.
header_block and sample_block have the same description?
…-docs Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
I added a note that this only supports quantitative phenotypes. I'm going to avoid making promises in our docs. |
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
henrydavidge
approved these changes
Jun 23, 2020
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
What changes are proposed in this pull request?
Creates documentation for WGR.
How is this patch tested?