cellink.io.read_plink

cellink.io.read_plink(path=None, *, var_rename=None, obs_rename=None, X_field='GT', hard_call=True, keep_multiallelic=False, load_call_fields=None, **kwargs)

Read Plink Format

Return type:

AnnData

Params

path

path to plink format

var_rename

mapping from sgkit’s variant annotation keys to desired gdata.var column

obs_rename

mapping from sgkit’s sample annotation keys to desired gdata.obs column

X_field

One of: “GT”, “DS”, “GP”, “MASK”, “AC”, “NONE”. - “GT”: collapsed allele count (sum of non-zero allele indices) -> X (samples, variants) - “DS”: scalar dosage (call_DS collapsed across alts) -> X - “GP”: argmax genotype state mapped to alt-count when mapping exists -> X - “MASK”: fraction of masked allele copies per (variant,sample) - “AC”: alias for “GT” - “NONE”: do not set X (X = np.empty((n_samples, 0))) or set to zeros? We set X to empty 2D dask array.

hard_call

if True, returns hard calls (0,1,2); if False, returns dosage/additive encoding

keep_multiallelic

if True, stores extra alternate alleles beyond ALT1; default is False

load_call_fields

iterable of call_* keys to load as layers; default None = load all present call_ fields.