shz9 / magenpy

Modeling and Analysis of (Statistical) Genetics data in python
https://shz9.github.io/magenpy/
MIT License
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Add support for reading summary statistics #1

Closed shz9 closed 2 years ago

shz9 commented 4 years ago

We need to add method to the GWASDataLoader class to read pre-computed summary statistics that can be obtained from other software tools (e.g. PLINK). The method should take either one big file and break into different chromosomes or 1 file per chromosome (as we do with the genotypes).

Sample summary statistics files can be found here: independent_sumstats.

Method signature is already written:

def read_summary_stats(self, sumstats_file):
    """
    TODO: implement reading functions for summary statistics
    """
    pass