magenpy 0.1.3

v0.1.3

on Python PyPI

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.