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Add an n_pcs option to run_platform_pca #468

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merged 1 commit into from
Jul 18, 2022
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Add an n_pcs option to run_platform_pca #468

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9 changes: 7 additions & 2 deletions gnomad/sample_qc/platform.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,9 @@ def compute_callrate_mt(


def run_platform_pca(
callrate_mt: hl.MatrixTable, binarization_threshold: Optional[float] = 0.25
callrate_mt: hl.MatrixTable,
binarization_threshold: Optional[float] = 0.25,
n_pcs: int = 10,
) -> Tuple[List[float], hl.Table, hl.Table]:
"""
Run PCA on a sample/interval MT with each entry containing the call rate.
Expand All @@ -91,6 +93,7 @@ def run_platform_pca(

:param callrate_mt: Input callrate MT
:param binarization_threshold: binzarization_threshold. None is no threshold desired
:param n_pcs: Number of PCs to compute
:return: eigenvalues, scores_ht, loadings_ht
"""
logger.info("Running platform PCA")
Expand All @@ -107,7 +110,9 @@ def run_platform_pca(
callrate=callrate_mt.callrate - callrate_mt.mean_callrate
)
eigenvalues, scores, loadings = hl.pca(
callrate_mt.callrate, compute_loadings=True
callrate_mt.callrate,
compute_loadings=True,
k=n_pcs,
) # TODO: Evaluate whether computing loadings is a good / worthy thing
logger.info("Platform PCA eigenvalues: %s", eigenvalues)

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