Releases
v0.1.3
shz9
released this
03 Jun 01:06
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.
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