cellink.tl.external.calculate_pcs

cellink.tl.external.calculate_pcs(dd, prefix, out=None, num_pcs=10, run=True, save_cmd_file=None, plink_export_kwargs={})

Run PLINK to calculate genetic PCs using the --pca option.

Parameters:

• dd (DonorData) – Object containing donor-level genotype (dd.G) and cell-level expression data (dd.C).

• prefix (str) – Prefix to PLINK binary files (.bed/.bim/.fam).

• out (str, optional) – Output file prefix. Defaults to <prefix>_pca.

• num_pcs (int, default=10) – Number of principal components to compute.

• run (bool, default=True) – If True, run the command. If False, return the command string.

• save_cmd_file (str, optional) – If provided, writes the command to a file.

• plink_export_kwargs (dict, optional) – Additional keyword arguments for to_plink function.

Return type:

DataFrame | str

Returns:

pd.DataFrame or str PC dataframe if run, or command string if run=False.