Make sample qc exprs return an array instead of a map #14
Conversation
This file contains hidden or 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
henrydavidge
force-pushed
the
sample-qc
branch
2 times, most recently
from
e91c91d to
4ce341a
Compare
henrydavidge
force-pushed
the
sample-qc
branch
from
4ce341a to
1ff61df
Compare
karenfeng
reviewed
Oct 16, 2019
Collaborator
karenfeng
left a comment
karenfeng
left a comment
There was a problem hiding this comment.
Couple of comments. Feel free to merge once addressed.
| } else { | ||
| new GenericArrayData(buffer.map { s => | ||
| val outputRow = new GenericInternalRow(MomentAggState.schema.length + 1) | ||
| s.momentAggState.toInternalRow(outputRow) |
Collaborator
There was a problem hiding this comment.
This stateful transformation is a little odd given that toInternalRow(outputRow) doesn't have a Unit return type - could we unify the way that we use this?
| override def dataType: DataType = MapType(StringType, MomentAggState.schema) | ||
|
|
||
| override def dataType: DataType = | ||
| if (optionalFieldIndices(0) != -1) { |
Collaborator
There was a problem hiding this comment.
We use optionalFieldIndices(0) == -1 throughout this class to refer to missing sample IDs - it'd be clearer to have a global val store this.
| def update(element: Int): Unit = update(element.toDouble) | ||
| def update(element: Float): Unit = update(element.toDouble) | ||
|
|
||
| def toInternalRow(row: InternalRow): InternalRow = { |
Collaborator
There was a problem hiding this comment.
Please add a comment stating that this will modify row
| } | ||
|
|
||
| private def readVcf(path: String): DataFrame = { | ||
| private def readVcf(path: String, includeSampleIds: Boolean = true): DataFrame = { |
Collaborator
There was a problem hiding this comment.
Do we test that the values are correct in the case that includeSampleIds = false?
| ) | ||
| if (includeSampleId) { | ||
| Array[Any]( | ||
| UTF8String.fromString(sampleId), |
Collaborator
There was a problem hiding this comment.
Can we prepend this value to the array of values that are always returned to avoid code duplication?
core/src/main/scala/io/projectglow/sql/expressions/PerSampleSummaryStatistics.scala
Outdated
Show resolved
Hide resolved
Signed-off-by: Henry D <henrydavidge@gmail.com>
3 tasks
henrydavidge
pushed a commit
to henrydavidge/glow
that referenced
this pull request
Jun 22, 2020
* Add type-checking to APIs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check valid alphas Signed-off-by: Karen Feng <karen.feng@databricks.com> * check 0 sig Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add to install_requires list Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup comments Signed-off-by: Karen Feng <karen.feng@databricks.com>
henrydavidge
pushed a commit
to henrydavidge/glow
that referenced
this pull request
Jun 22, 2020
* Add option to provide sample IDs * Include genotype from VCF * Read sample IDs from extra/overrideHeaderLines * Address comments * Replace header option * Address comments, clean up options Signed-off-by: Henry Davidge <hhd@databricks.com>
henrydavidge
added a commit
to henrydavidge/glow
that referenced
this pull request
Jun 22, 2020
* some work Make sample qc return an array instead of a map Signed-off-by: Henry D <henrydavidge@gmail.com> * fix test Signed-off-by: Henry D <henrydavidge@gmail.com> * karen's comments Signed-off-by: Henry D <henrydavidge@gmail.com> Signed-off-by: Henry Davidge <hhd@databricks.com>
henrydavidge
pushed a commit
to henrydavidge/glow
that referenced
this pull request
Jun 22, 2020
* Add type-checking to APIs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check valid alphas Signed-off-by: Karen Feng <karen.feng@databricks.com> * check 0 sig Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add to install_requires list Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup comments Signed-off-by: Karen Feng <karen.feng@databricks.com> Signed-off-by: Henry Davidge <hhd@databricks.com>
henrydavidge
added a commit
that referenced
this pull request
Jun 22, 2020
* Add Leland's demo notebook * block_variants_and_samples Transformer to create genotype DataFrame for WGR (#2) * blocks Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test vcf Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * transformer Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * remove extra Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * refactor and conform with ridge namings Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test files Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * remove extra file Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * sort_key Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * feat: ridge models for wgr added (#1) * feat: ridge models for wgr added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Doc strings added for levels/functions.py Some typos fixed in ridge_model.py Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * ridge_model and RidgeReducer unit tests added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * RidgeRegression unit tests added test data README added ridge_udfs.py docstrings added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * 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 (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * 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 (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * [HLS-539] Fix compatibility between blocked GT transformer and WGR (#6) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * existing tests pass Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename file Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add compat test Signed-off-by: Karen Feng <karen.feng@databricks.com> * scalafmt Signed-off-by: Karen Feng <karen.feng@databricks.com> * collect minimal columns Signed-off-by: Karen Feng <karen.feng@databricks.com> * address comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Test fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Spark 3 needs more recent PyArrow, reduce mem consumption by removing unnecessary caching Signed-off-by: Karen Feng <karen.feng@databricks.com> * PyArrow 0.15.1 only with PySpark 3 Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't use toPandas() Signed-off-by: Karen Feng <karen.feng@databricks.com> * Upgrade pyarrow Signed-off-by: Karen Feng <karen.feng@databricks.com> * Only register once Signed-off-by: Karen Feng <karen.feng@databricks.com> * Minimize memory usage Signed-off-by: Karen Feng <karen.feng@databricks.com> * Select before head Signed-off-by: Karen Feng <karen.feng@databricks.com> * set up/tear down Signed-off-by: Karen Feng <karen.feng@databricks.com> * Try limiting pyspark memory Signed-off-by: Karen Feng <karen.feng@databricks.com> * No teardown Signed-off-by: Karen Feng <karen.feng@databricks.com> * Extend timeout Signed-off-by: Karen Feng <karen.feng@databricks.com> * Simplify ordering logic in levels code (#7) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * existing tests pass Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename file Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add compat test Signed-off-by: Karen Feng <karen.feng@databricks.com> * scalafmt Signed-off-by: Karen Feng <karen.feng@databricks.com> * collect minimal columns Signed-off-by: Karen Feng <karen.feng@databricks.com> * start changing for readability * use input label ordering * rename create_row_indexer * undo column sort * change reduce Signed-off-by: Henry D <henrydavidge@gmail.com> * further simplify reduce * sorted alpha names * remove ordering * comments Signed-off-by: Henry D <henrydavidge@gmail.com> * Set arrow env var in build Signed-off-by: Henry D <henrydavidge@gmail.com> * faster sort * add test file * undo test data change * >= * formatting * empty Co-authored-by: Karen Feng <karen.feng@databricks.com> * Limit Spark memory conf in tests (#9) * yapf Signed-off-by: Karen Feng <karen.feng@databricks.com> * yapf transform Signed-off-by: Karen Feng <karen.feng@databricks.com> * Set driver memory Signed-off-by: Karen Feng <karen.feng@databricks.com> * Try changing spark mem Signed-off-by: Karen Feng <karen.feng@databricks.com> * match java tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * remove driver memory flag Signed-off-by: Karen Feng <karen.feng@databricks.com> * Improve partitioning in block_variants_and_samples transformer (#11) Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * Remove unnecessary header_block grouping (#10) * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Create sample ID blocking helper functions (#12) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * simplify tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * yapf Signed-off-by: Karen Feng <karen.feng@databricks.com> * index map compat Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add more tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * pass args as ints Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't roll our own splitter Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename sample_index to sample_blocks Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add type-checking to WGR APIs (#14) * Add type-checking to APIs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check valid alphas Signed-off-by: Karen Feng <karen.feng@databricks.com> * check 0 sig Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add to install_requires list Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add covariate support (#13) * 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 (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Cleaned up one unnecessary Pandas import Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Small changes for clarity and consistence with the rest of the code. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Forgot one usage of coalesce Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Added a couple of comments to explain logic and replaced usages of .values with .array Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Fixed one instance of the change .values -> .array where it was made in error. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Typo in test_ridge_regression.py. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Style auto-updates with yapfAll Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> Co-authored-by: Leland Barnard <leland.barnard@regeneron.com> Co-authored-by: Karen Feng <karen.feng@databricks.com> * Flatten estimated phenotypes (#15) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Clean up tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Order to match labeldf Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check we tie-break Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * test var name Signed-off-by: Karen Feng <karen.feng@databricks.com> * clean up tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * Clean up docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add fit_transform function to models (#17) Signed-off-by: Karen Feng <karen.feng@databricks.com> * Rename levels (#20) * Rename levels to wgr Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename test files Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add license headers (#21) * headers * executable * fix template rendering * yapf * add header to template * add header to template Signed-off-by: Henry D <henrydavidge@gmail.com> Co-authored-by: Kiavash Kianfar <kiavash.kianfar@databricks.com> Co-authored-by: Karen Feng <karen.feng@databricks.com> Co-authored-by: Leland <leland.barnard@gmail.com> Co-authored-by: Leland Barnard <leland.barnard@regeneron.com>
henrydavidge
added a commit
that referenced
this pull request
Jun 22, 2020
* Add Leland's demo notebook * block_variants_and_samples Transformer to create genotype DataFrame for WGR (#2) * blocks Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test vcf Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * transformer Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * remove extra Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * refactor and conform with ridge namings Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test files Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * remove extra file Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * sort_key Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * feat: ridge models for wgr added (#1) * feat: ridge models for wgr added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Doc strings added for levels/functions.py Some typos fixed in ridge_model.py Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * ridge_model and RidgeReducer unit tests added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * RidgeRegression unit tests added test data README added ridge_udfs.py docstrings added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * 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 (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * 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 (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * [HLS-539] Fix compatibility between blocked GT transformer and WGR (#6) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * existing tests pass Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename file Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add compat test Signed-off-by: Karen Feng <karen.feng@databricks.com> * scalafmt Signed-off-by: Karen Feng <karen.feng@databricks.com> * collect minimal columns Signed-off-by: Karen Feng <karen.feng@databricks.com> * address comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Test fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Spark 3 needs more recent PyArrow, reduce mem consumption by removing unnecessary caching Signed-off-by: Karen Feng <karen.feng@databricks.com> * PyArrow 0.15.1 only with PySpark 3 Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't use toPandas() Signed-off-by: Karen Feng <karen.feng@databricks.com> * Upgrade pyarrow Signed-off-by: Karen Feng <karen.feng@databricks.com> * Only register once Signed-off-by: Karen Feng <karen.feng@databricks.com> * Minimize memory usage Signed-off-by: Karen Feng <karen.feng@databricks.com> * Select before head Signed-off-by: Karen Feng <karen.feng@databricks.com> * set up/tear down Signed-off-by: Karen Feng <karen.feng@databricks.com> * Try limiting pyspark memory Signed-off-by: Karen Feng <karen.feng@databricks.com> * No teardown Signed-off-by: Karen Feng <karen.feng@databricks.com> * Extend timeout Signed-off-by: Karen Feng <karen.feng@databricks.com> * Simplify ordering logic in levels code (#7) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * existing tests pass Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename file Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add compat test Signed-off-by: Karen Feng <karen.feng@databricks.com> * scalafmt Signed-off-by: Karen Feng <karen.feng@databricks.com> * collect minimal columns Signed-off-by: Karen Feng <karen.feng@databricks.com> * start changing for readability * use input label ordering * rename create_row_indexer * undo column sort * change reduce Signed-off-by: Henry D <henrydavidge@gmail.com> * further simplify reduce * sorted alpha names * remove ordering * comments Signed-off-by: Henry D <henrydavidge@gmail.com> * Set arrow env var in build Signed-off-by: Henry D <henrydavidge@gmail.com> * faster sort * add test file * undo test data change * >= * formatting * empty Co-authored-by: Karen Feng <karen.feng@databricks.com> * Limit Spark memory conf in tests (#9) * yapf Signed-off-by: Karen Feng <karen.feng@databricks.com> * yapf transform Signed-off-by: Karen Feng <karen.feng@databricks.com> * Set driver memory Signed-off-by: Karen Feng <karen.feng@databricks.com> * Try changing spark mem Signed-off-by: Karen Feng <karen.feng@databricks.com> * match java tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * remove driver memory flag Signed-off-by: Karen Feng <karen.feng@databricks.com> * Improve partitioning in block_variants_and_samples transformer (#11) Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * Remove unnecessary header_block grouping (#10) * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Create sample ID blocking helper functions (#12) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * simplify tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * yapf Signed-off-by: Karen Feng <karen.feng@databricks.com> * index map compat Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add more tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * pass args as ints Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't roll our own splitter Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename sample_index to sample_blocks Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add type-checking to WGR APIs (#14) * Add type-checking to APIs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check valid alphas Signed-off-by: Karen Feng <karen.feng@databricks.com> * check 0 sig Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add to install_requires list Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add covariate support (#13) * 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 (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Cleaned up one unnecessary Pandas import Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Small changes for clarity and consistence with the rest of the code. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Forgot one usage of coalesce Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Added a couple of comments to explain logic and replaced usages of .values with .array Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Fixed one instance of the change .values -> .array where it was made in error. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Typo in test_ridge_regression.py. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Style auto-updates with yapfAll Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> Co-authored-by: Leland Barnard <leland.barnard@regeneron.com> Co-authored-by: Karen Feng <karen.feng@databricks.com> * Flatten estimated phenotypes (#15) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Clean up tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Order to match labeldf Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check we tie-break Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * test var name Signed-off-by: Karen Feng <karen.feng@databricks.com> * clean up tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * Clean up docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add fit_transform function to models (#17) Signed-off-by: Karen Feng <karen.feng@databricks.com> * support alpha inference Signed-off-by: Karen Feng <karen.feng@databricks.com> * test fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * more test fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * test fixups Signed-off-by: Karen Feng <karen.feng@databricks.com> * sub-sample Signed-off-by: Karen Feng <karen.feng@databricks.com> * test fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * address comments - only infer alphas during fit Signed-off-by: Karen Feng <karen.feng@databricks.com> * exception varies Signed-off-by: Karen Feng <karen.feng@databricks.com> * Rename levels (#20) * Rename levels to wgr Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename test files Signed-off-by: Karen Feng <karen.feng@databricks.com> * Errors vary by Spark version Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add license headers (#21) * headers * executable * fix template rendering * yapf Co-authored-by: Kiavash Kianfar <kiavash.kianfar@databricks.com> Co-authored-by: Karen Feng <karen.feng@databricks.com> Co-authored-by: Leland <leland.barnard@gmail.com> Co-authored-by: Leland Barnard <leland.barnard@regeneron.com>
karenfeng
added a commit
that referenced
this pull request
Jun 23, 2020
* Add Leland's demo notebook * block_variants_and_samples Transformer to create genotype DataFrame for WGR (#2) * blocks Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test vcf Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * transformer Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * remove extra Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * refactor and conform with ridge namings Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * test files Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * remove extra file Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * sort_key Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * feat: ridge models for wgr added (#1) * feat: ridge models for wgr added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Doc strings added for levels/functions.py Some typos fixed in ridge_model.py Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * ridge_model and RidgeReducer unit tests added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * RidgeRegression unit tests added test data README added ridge_udfs.py docstrings added Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * 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 (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * 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 (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * [HLS-539] Fix compatibility between blocked GT transformer and WGR (#6) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * existing tests pass Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename file Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add compat test Signed-off-by: Karen Feng <karen.feng@databricks.com> * scalafmt Signed-off-by: Karen Feng <karen.feng@databricks.com> * collect minimal columns Signed-off-by: Karen Feng <karen.feng@databricks.com> * address comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Test fixup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Spark 3 needs more recent PyArrow, reduce mem consumption by removing unnecessary caching Signed-off-by: Karen Feng <karen.feng@databricks.com> * PyArrow 0.15.1 only with PySpark 3 Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't use toPandas() Signed-off-by: Karen Feng <karen.feng@databricks.com> * Upgrade pyarrow Signed-off-by: Karen Feng <karen.feng@databricks.com> * Only register once Signed-off-by: Karen Feng <karen.feng@databricks.com> * Minimize memory usage Signed-off-by: Karen Feng <karen.feng@databricks.com> * Select before head Signed-off-by: Karen Feng <karen.feng@databricks.com> * set up/tear down Signed-off-by: Karen Feng <karen.feng@databricks.com> * Try limiting pyspark memory Signed-off-by: Karen Feng <karen.feng@databricks.com> * No teardown Signed-off-by: Karen Feng <karen.feng@databricks.com> * Extend timeout Signed-off-by: Karen Feng <karen.feng@databricks.com> * Simplify ordering logic in levels code (#7) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * existing tests pass Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename file Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add compat test Signed-off-by: Karen Feng <karen.feng@databricks.com> * scalafmt Signed-off-by: Karen Feng <karen.feng@databricks.com> * collect minimal columns Signed-off-by: Karen Feng <karen.feng@databricks.com> * start changing for readability * use input label ordering * rename create_row_indexer * undo column sort * change reduce Signed-off-by: Henry D <henrydavidge@gmail.com> * further simplify reduce * sorted alpha names * remove ordering * comments Signed-off-by: Henry D <henrydavidge@gmail.com> * Set arrow env var in build Signed-off-by: Henry D <henrydavidge@gmail.com> * faster sort * add test file * undo test data change * >= * formatting * empty Co-authored-by: Karen Feng <karen.feng@databricks.com> * Limit Spark memory conf in tests (#9) * yapf Signed-off-by: Karen Feng <karen.feng@databricks.com> * yapf transform Signed-off-by: Karen Feng <karen.feng@databricks.com> * Set driver memory Signed-off-by: Karen Feng <karen.feng@databricks.com> * Try changing spark mem Signed-off-by: Karen Feng <karen.feng@databricks.com> * match java tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * remove driver memory flag Signed-off-by: Karen Feng <karen.feng@databricks.com> * Improve partitioning in block_variants_and_samples transformer (#11) Signed-off-by: kianfar77 <kiavash.kianfar@databricks.com> * Remove unnecessary header_block grouping (#10) * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Create sample ID blocking helper functions (#12) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * whoops Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * simplify tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * yapf Signed-off-by: Karen Feng <karen.feng@databricks.com> * index map compat Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add more tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * pass args as ints Signed-off-by: Karen Feng <karen.feng@databricks.com> * Don't roll our own splitter Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename sample_index to sample_blocks Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add type-checking to WGR APIs (#14) * Add type-checking to APIs Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check valid alphas Signed-off-by: Karen Feng <karen.feng@databricks.com> * check 0 sig Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add to install_requires list Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add covariate support (#13) * 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 (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Cleaned up one unnecessary Pandas import Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Small changes for clarity and consistence with the rest of the code. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Forgot one usage of coalesce Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Added a couple of comments to explain logic and replaced usages of .values with .array Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Fixed one instance of the change .values -> .array where it was made in error. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Typo in test_ridge_regression.py. Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> * Style auto-updates with yapfAll Signed-off-by: Leland Barnard (leland.barnard@gmail.com) Signed-off-by: Leland Barnard <leland.barnard@regeneron.com> Co-authored-by: Leland Barnard <leland.barnard@regeneron.com> Co-authored-by: Karen Feng <karen.feng@databricks.com> * Flatten estimated phenotypes (#15) * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Clean up tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Order to match labeldf Signed-off-by: Karen Feng <karen.feng@databricks.com> * Check we tie-break Signed-off-by: Karen Feng <karen.feng@databricks.com> * cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * test var name Signed-off-by: Karen Feng <karen.feng@databricks.com> * clean up tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * Clean up docs Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * remove accidental files Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add fit_transform function to models (#17) Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * Rename levels (#20) * Rename levels to wgr Signed-off-by: Karen Feng <karen.feng@databricks.com> * rename test files Signed-off-by: Karen Feng <karen.feng@databricks.com> * Add license headers (#21) * headers * executable * fix template rendering * yapf * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * WIP Signed-off-by: Karen Feng <karen.feng@databricks.com> * More work Signed-off-by: Karen Feng <karen.feng@databricks.com> * More cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * Fix docs tests Signed-off-by: Karen Feng <karen.feng@databricks.com> * address comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * fix regression fit description Signed-off-by: Karen Feng <karen.feng@databricks.com> * fix capitalization Signed-off-by: Karen Feng <karen.feng@databricks.com> * address some comments Signed-off-by: Karen Feng <karen.feng@databricks.com> * more cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * More cleanup Signed-off-by: Karen Feng <karen.feng@databricks.com> * add notebook Signed-off-by: Karen Feng <karen.feng@databricks.com> * update notebook Signed-off-by: Karen Feng <karen.feng@databricks.com> Co-authored-by: Henry D <henrydavidge@gmail.com> Co-authored-by: Kiavash Kianfar <kiavash.kianfar@databricks.com> Co-authored-by: Leland <leland.barnard@gmail.com> Co-authored-by: Leland Barnard <leland.barnard@regeneron.com>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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?
Now that apache/spark#25666 has merged, it's more convenient and performant to return an array and filter by index. In addition, we can now generate sample qc stats when we don't have sample ids, which we expect to be the common case.
How is this patch tested?
(Details)