pandas_genomics.accessors.GenotypeSeriesAccessor

class pandas_genomics.accessors.GenotypeSeriesAccessor(obj)

Series accessor for GenotypeArray methods

s.genomics.variant_info
s.genomics.encode_additive()

__init__(obj)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(obj)	Initialize self.
calculate_edge_encoding_values(data, …[, …])	Calculate alpha values to be used in weighted encoding
contained_by(regions)	True if the variant is contained within the specified region(s)
encode_additive()	Additive encoding of genotypes.
encode_codominant()	Codominant encoding of genotypes.
encode_dominant()	Dominant encoding of genotypes.
encode_edge(alpha_value, ref_allele, …)	EDGE (weighted) encoding of genotypes.
encode_recessive()	Recessive encoding of genotypes.
set_reference(allele)	Change the allele reference variant.

Attributes

gt_scores	Return an array of genotype scores as float values np.nan when the score is missing
hwe_pval	Return the probability that the samples are in HWE
maf	Return the minor allele frequency
variant	Retrieve the variant object
variant_info	Retrieve the variant as a pandas Series