GenotypePhenotypeMap

The GenotypePhenotypeMap class is main entry-point to the gpmap package. It offers intuitive and useful methods and attributes for analyzing genotype-phenotype data. We’ve also created a number of other packages that easily interact with the GenotypePhenotypeMap.

Example

from gpmap import GenotypePhenotypeMap

# Create list of genotypes and phenotypes
wildtype = "AA"
genotypes = ["AA", "AV", "AM", "VA", "VV", "VM"]
phenotypes = [1.0, 1.1, 1.4, 1.5, 2.0, 3.0]

# Create GenotypePhenotypeMap object
gpm = GenotypePhenotypeMap(wildtype, genotypes, phenotypes)

BinaryMap

All GenotypePhenotypeMap objects append a BinaryMap instance to a the binary attribute. The BinaryMap class creates a binary representation of all genotypes and maps them to a genotype-phenotype map. Most attributes in the GenotypePhenotypeMap also exist in the binary object, updated with the binary genotype representations.