cellink.io.to_plink

cellink.io.to_plink(gdata, output_prefix=None, donor_id='donor_id', donor_family_id='donor_family_id', donor_paternal_id='donor_paternal_id', donor_maternal_id='donor_maternal_id', donor_sex='sex', chrom='chrom', pos='pos', a0='a0', a1='a1')

Export genotype data from an AnnData object to PLINK1 binary format (.bed, .bim, .fam).

Parameters:

• gdata (anndata.AnnData) – AnnData object containing genotype data in .X, with variants in .var and sample metadata in .obs.

• output_prefix (str) – Prefix for the output PLINK files. If it does not end with ‘.bed’, the extension is appended automatically.

• donor_id (str, default DAnn.donor) – Column in gdata.obs representing sample (individual) IDs.

• donor_family_id (str, default DAnn.donor_family) – Column in gdata.obs representing family IDs. If not present, donor_id is used instead.

• donor_paternal_id (str, default DAnn.donor_paternal_id) – Column in gdata.obs representing paternal IDs. If not found, all values will default to 0.

• donor_maternal_id (str, default DAnn.donor_maternal_id) – Column in gdata.obs representing maternal IDs. If not found, all values will default to 0.

• donor_sex (str, default "sex") – Column in gdata.obs representing sample sex. Must be coded as: 1=male, 2=female, 0=unknown. If not found, all values will default to 0.

• chrom (str, default VAnn.chrom) – Column in gdata.var representing chromosome information.

• pos (str, default VAnn.pos) – Column in gdata.var representing base-pair positions.

• a0 (str, default VAnn.a0) – Column in gdata.var representing the reference allele.

• a1 (str, default VAnn.a1) – Column in gdata.var representing the alternate allele.

Return type:

None

Returns:

None Writes .bed, .bim, and .fam files to disk using the provided prefix.

Notes

• Uses xarray to construct a labeled data array of genotypes.

• Internally calls sgkit.io.plink.write_plink1_bin for exporting to PLINK format.