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)