cellink.tl.external.make_group_file

cellink.tl.external.make_group_file(dd=None, region_file=None, output_prefix='group_file', allele_order='alt-first', run=True, save_cmd_file=None, plink_export_kwargs=None, remove_intermediate_files=True, runner=None)

Create group file for set-based rare variant tests.

Parameters:

• dd (DonorData, optional) – DonorData object. If provided, will export to PLINK format.

• region_file (str) – Path to region file (chr, start, end; no header)

• output_prefix (str) – Output file prefix

• allele_order (str, default="alt-first") – Allele order for PLINK/BGEN

• run (bool, default=True) – Whether to execute command

• save_cmd_file (str, optional) – Save command to file

• plink_export_kwargs (dict, optional) – Additional kwargs for to_plink

• remove_intermediate_files (bool, default=True) – Remove intermediate PLINK files

• runner (SAIGEQTLRunner, optional) – Runner instance

Return type:

str

Returns:

str Path to group file or command string