admix.Dataset

class admix.Dataset(geno: Array | None = None, lanc: Array | None = None, snp: DataFrame | None = None, indiv: DataFrame | None = None, n_anc: int | None = None, dset_ref=None, snp_idx: slice | int | ndarray | None = None, indiv_idx: slice | int | ndarray | None = None, enforce_order: bool = True)

Data structure to contain genotype and local ancestry.

__init__(geno: Array | None = None, lanc: Array | None = None, snp: DataFrame | None = None, indiv: DataFrame | None = None, n_anc: int | None = None, dset_ref=None, snp_idx: slice | int | ndarray | None = None, indiv_idx: slice | int | ndarray | None = None, enforce_order: bool = True)

Methods

__init__([geno, lanc, snp, indiv, n_anc, ...])
af_per_anc([force])	Return the allele frequency per ancestry (n_snp, n_anc)
allele_per_anc()	Return the allele-per-ancestry raw count matrix
append_indiv_info(df_info[, force_update])	append indiv info to the dataset, individual is matched using the self.indiv.index and df_info.index.
append_snp_info(df_info)	append snp info to the dataset, snp is matched using the self.snp.index and df_info.index.
nhaplo_per_anc([force])	Return the number of haplotype per ancestry (n_snp, n_anc)
persist()	persist the lazy data to memory

Attributes

data	Number of individuals.
geno	Genotype matrix
indiv	One-dimensional annotation of observations (pd.DataFrame).
lanc	Local ancestry matrix
n_anc	Number of ancestries.
n_indiv	Number of individuals.
n_snp	Number of SNPs.
snp	One-dimensional annotation of observations (pd.DataFrame).
uns	Unstructured annotation (ordered dictionary).
xr	Return the xr.Dataset used internally