sushie.cli.parameter_check(args: Namespace) → Tuple[int, DataFrame, List[str], DataFrame, List[str], Callable][source]
The function to process raw phenotype, genotype, covariates data across ancestries

for individual-level data fine-mapping.

Parameters:
args: Namespace

The command line parameter input.

Returns:

A tuple of

  1. an integer to indicate how many ancestries,

  2. a DataFrame that contains ancestry index (can be none),

  3. a list that contains subject ID that fine-mapping performs on.

  4. a DataFrame that contains prior probability for each SNP to be causal.

  5. a list of genotype data paths (List[str]),

  6. genotype read-in function (Callable).

Return type:

Tuple[int, pd.DataFrame, List[str], Callable]

Last update: Oct 27, 2024