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()
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)