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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.1.4] - 2024-10-01

Changed

  • Updated the data type for the index pointer in the LDMatrix object to be int64. int32 does not work well for very large datasets with millions of variants and it causes overflow errors.
  • Updated the way we determine the pandas chunksize when converting from plink tables to zarr.
  • Simplified the way we compute the quantization scale in model_utils.
  • Fixed major bug in how LD window thresholds that are passed to plink1.9 are computed.
  • Fixed in-place fillna in from_plink_table in LDMatrix to conform to latest pandas API.
  • Update run_shell_script to check for and capture errors.
  • Refactored code to slightly reduce import/load times.
  • Cleaned up load_data method of LDMatrix and subsumed functionality in load_rows.
  • Fixed bugs in match_snp_tables.
  • Fixed bugs and re-wrote how the block LD estimator is computed using both the plink and xarray backends.
  • Updated from_plink_table method in LDMatrix to handle cases where boundaries are different from what plink computes.
  • Fixed bug in symmetrize_ut_csr_matrix utility functions.
  • Changed default storage data type for LD matrices to int16.

Added

  • Added extra validation checks in LDMatrix to ensure that the index pointer is formatted correctly.
  • LDLinearOperator class to allow for efficient linear algebra operations on the LD matrix without representing the full symmetric matrix in memory.
  • Added utility methods to LDMatrix class to allow for computing eigenvalues, performing SVD, etc.
  • Added Spectral properties to the attributes of LD matrices.
  • Added support to slice/retrieve entries of LD matrix by using SNP rsIDs.
  • Added support to reading LD matrices from AWS s3 storage.
  • Added utility method to detect if a file contains header information.
  • Added utility method to generate overlapping windows over a sequence.
  • Added compute_extremal_eigenvalues to allow the user to compute extremal (minimum and maximum) eigenvalues of LD matrices.
  • Added the utility function combine_ld_matrices to allow for combining LD matrices from different sources.

[0.1.3] - 2024-05-21

Changed

  • Updated the logic for detect_outliers in phenotype transforms to actually reflect the function name (before it was returning true for inliers...).
  • Updated quantize and dequantize to minimize data copying as much as possible.
  • Updated LDMatrix.load_rows() method to minimize data copying.
  • Fixed bug in LDMatrix.n_neighbors implementation.
  • Updated dask version in requirements.txt to avoid installing dask-expr.

Added

  • Added get_peak_memory_usage to system_utils to inspect peak memory usage of a process.
  • Placeholder method to perform QC on SumstatsTable objects (needs to be implemented still).
  • New attached dataset for long-range LD regions.
  • New method in SumstatsTable to impute rsID (if missing).
  • Preliminary support for matching with CHR+POS in SumstatsTable (still needs more work).
  • LDMatrix updates:
    • New method to filter long-range LD regions.
    • New method to prune LD matrix.
  • New algorithm for symmetrizing upper triangular and block diagonal LD matrices.
    • Much faster and more memory efficient than using scipy.
    • New LDMatrix class has efficient data loading in .load_data method.
    • We still retain load_rows because it is useful for loading a subset of rows.

[0.1.2] - 2024-04-24

Changed

  • Fixed manhattan plot implementation to support various new features.
  • Added a warning when accessing csr_matrix property of LDMatrix when it hasn't been loaded previously.

Added

  • reset_mask method for magenpy LDMatrix.
  • Dockerfiles for both cli and jupyter modes.
  • A helper script to convert LD matrices from old format to new format.

[0.1.1] - 2024-04-12

Changed

  • Fixed bugs in how covariates are processed in SampleTable.
  • Fixed bugs / issues in implementation of GWAS with xarray backend.
  • Streamlined implementation of manhattan plotting function.

[0.1.0] - 2024-04-04

A large scale restructuring of the code base to improve efficiency and usability.

Changed

  • Bug fixes across the entire code base.
  • Simulator classes have been renamed from GWASimulator to PhenotypeSimulator.
  • Moved plotting script to its own separate module.
  • Updated some method names / commandline flags to be consistent throughout.

Added

  • Basic integration testing with pytest and GitHub workflows.
  • Documentation for the entire package using mkdocs.
  • Integration testing / automating building with GitHub workflows.
  • New implementation of the LD matrix that uses CSR matrix data structures.
    • Quantization / float precision specification when storing LD matrices.
    • Allow user to specify Compressor / Compressor options for Zarr storage.
  • New implementation of magenpy_simulate script.
    • Allow users to set random seed.
    • Now accept --prop-causal instead of specifying full mixing proportions.
  • Tried to incorporate genome_build into various data structures. This will be useful in the future to ensure consistent genome builds across different data types.
  • Allow user to pass various metadata to magenpy_ld to save information about dataset characteristics.
  • New sumstats parsers:
    • Saige sumstats format.
    • plink1.9 sumstats format.
    • GWAS Catalog sumstats format.
  • Chained transform function for transforming phenotypes.

[0.0.12] - 2023-02-12

Changed

  • Removed the --fast-math compiler flag due to concerns about numerical precision (e.g. Beware of fast-math).
  • Updated implementation of SumstatsParser class to allow user to specify read_csv_kwargs at the point of instantiation.
  • Updated plink executors to propagate the error messages to the user.
  • Updated merge_snp_tables to allow for merges on columns other than SNP.
  • Refactored, cleaned, and updated the implementation of the AnnotationMatrix class.
  • Fixed bug in GWADataLoader.split_by_samples(): Need to perform deepcopy, otherwise splitting would not work properly.
  • Updated read_annotations method in GWADataLoader to work with the latest AnnotationMatrix interfaces.
  • Fixed bug in the manhattan plotting function.

Added

  • Added parsers for functional annotations and annotation files. Mainly support LDSC annotation format for now.
  • Added a utility method to GWADataLoader called align_with to streamline aligning GWADataLoader objects across SNP and sample dimensions.
  • Added utility methods for flattening the LD matrix in LDMatrix.
  • Added a method to perform matrix-vector multiplication in LDMatrix.
  • Added a method to perform block-wise iteration in the LDMatrix class.

[0.0.11] - 2022-09-06

Changed

  • Fixed bug in implementation of identify_mismatched_snps.
  • Fixed bugs in handling of missing information in LD matrix.
  • Fixed bug in handling of covariates in SampleTable.
  • Updated README file to remove line indicators >>> from sample code.

Added

  • Added the reference allele A2 to the output of the true_beta_table in GWASimulator.

[0.0.10] - 2022-08-22

Changed

  • Fixed a bug in the phenotype likelihood inference in SampleTable.
  • Changed the implementation of the merge_snp_tables utility function to check for BOTH reference and alternative alleles.
  • Modified implementation of score method of GWADataLoader to correct potential issues with the BETAS being for a subset of the chromosomes.

Added

  • A utility method to GenotypeMatrix called estimate_memory_allocation. This should allow the user to gauge the memory resources required to interact with the genotype files.

[0.0.9] - 2022-08-09

Changed

  • Fixing bug in computing minor allele frequency with plink.

[0.0.8] - 2022-08-09

Added

  • Added the reference allele A2 to the list of attributes of LDMatrix.
  • Added effect_sign as a property of SumstatsTable.

Changed

  • Fixed implementation of merge_snp_tables to detect allele differences that are not flips between A1/A2.
  • Improved implementation of .score method of xarrayGenotypeMatrix.

[0.0.7] - 2022-07-12

Added

  • Added tqdm progress bars when processing multiple files/chromosomes in GWADataLoader.
  • Added min_maf and min_mac flags in magenpy_ld and magenpy_simulate.

Changed

  • Lowered default threshold for LD shrinkage to 1e-3.
  • Bug fix in SampleTable.

[0.0.6] - 2022-07-11

Added

  • Utility function to compute the genomic control or lambda factor.
  • A method to set the causal SNPs directly in GWASimulator.

Changed

  • Fixed bugs in manhattan plotting function.
  • Added alternative ways to derive Chi-Squared statistic from other summary stats (e.g. p-value).
  • Give user more fine-grained control on what to reset in the .simulate() method of GWASimulator.
  • Modified the LD score computation method to allow for aggregating LD scores by functional category or annotations.
  • Streamlining module import structure to speed up loading.

[0.0.5] - 2022-06-28

Changed

  • Fixed bugs in rechunking logic when computing LD matrices using xarray/dask

[0.0.4] - 2022-06-28

Added

  • A new attached dataset of GWAS summary statistics for standing height from the fastGWA database.

Changed

  • Updated the data harmonization method in GWADataLoader to ensure that all data sources have the same set of chromosomes.
  • Bug fixes in SumStatsTable, GWASimulator, and GWADataLoader.

[0.0.3] - 2022-06-26

Added

  • New methods to split GWADataLoader objects by chromosome and by samples. The latter should come in handy for splitting the samples for training, validation and testing.

Changed

  • Updated implementation of the shrinkage estimator of LD to align it more closely with the original formulation in Wen and Stephens (2010) and implementations in RSS software.
  • Fixed various bugs and errors in the code.
  • Added proper handling for the slice objects in plot_ld_matrix

[0.0.2] - 2022-06-15

Added

  • Added classes encapsulating data structures and methods for:

    • Genotype matrices: GenotypeMatrix
    • Sample tables: SampleTable
    • Summary statistics table: SumstatsTable

  • Added a new stats submodule that implements utilities and functions to compute various statistics, including ld (SNP correlation matrix), h2 (heritability), score, transforms, variant statistics, and gwa (genome-wide association testing).

  • Added a modular class for summary statistics parsers SumstatsParser.

  • Added modular interfaces for executors, representing external software, such as plink.

  • Added support for window size specifications using number of SNPs and distance in kilobases.

  • Added CHANGELOG.md to track the latest changes and updates to magenpy.

Changed

  • Refactored the GWADataLoader class to utilize the new data structures.
  • Updated plotting functions/utilities.
  • Updated documentation in README file.
  • Updated implementation of MulticohortGWASimulator (still incomplete).

[0.0.1] - 2022-05-17

Added

  • Refactored the code for pypi package release.
  • Added license, .toml file, and MANIFEST.in.

Changed

  • Updated setup.py to prepare for the package release.
  • Updated README.md to add basic documentation.