pandas_genomics.accessors.GenotypeDataframeAccessor

class pandas_genomics.accessors.GenotypeDataframeAccessor(pandas_obj)[source]

DataFrame accessor for GenotypeArray methods

df.genomics.variant_info
df.genomics.encode_additive()
__init__(pandas_obj)[source]

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

Methods

__init__(pandas_obj)

Initialize self.

calculate_edge_encoding_values(data, …[, …])

Calculate alpha values to be used in edge encoding

encode_additive()

Additive encoding of genotypes.

encode_codominant()

Codominant encoding of genotypes.

encode_dominant()

Dominant encoding of genotypes.

encode_edge(encoding_info)

EDGE (weighted) encoding of genotypes.

encode_recessive()

Recessive encoding of genotypes.

filter_variants_hwe([cutoff])

Drop variants with a probability of HWE less than the specified value (0.05 by default).

filter_variants_maf([keep_min_freq])

Drop variants with a MAF less than the specified value (0.01 by default)

in_regions(regions)

Keep variants that exist in one or more of the specified regions

not_in_regions(regions)

Remove variants that exist in one or more of the specified regions

Attributes

hwe_pval

Return the probability that the samples are in HWE

maf

Return the minor allele frequency of each variant

variant_info

Return a DataFrame with variant info indexed by the column name (one row per GenotypeArray)