Working with PED files

The PED class

PED(PED, MAP, encoder = None):


PED - The ped file containing the genotype data.

MAP - The map file which contains labels for the snps in the ped file.

encoder - A pandas series which contains the reference/alternate alleles (eg. ‘A/G’) for each position with ids that correspond to the file. Defaults to None. Must provide one in order to get a genotype matrix.


Data that was passed in parsed as a pandas dataframe.
The map file parsed as a pandas dataframe.
A pandas dataframe of the genotype data. 0 represents homozygous for the reference allele, 1 is heterozygous, and 2 is homozygous for the alternate allele.