This class provides a minimal and fast interface for retrieving genotypes from Plinks's BED/BIM/FAM file trios. The BED file must fit in memory.
numpy, pandas, and numba. These are included with many Python
distributions.
Run pip install microplink or clone this repository and run python setup.py install from the repository directory.
Typical usage:
import microplink as mic
# Equivalent to `pf = mic.PlinkFiles('test.bed', 'test.bim', 'test.fam')`
pf = mic.PlinkFiles('test')
# fetch by chromosome and position
pf.get_genotypes(chromosome=1, position=10000)
# fetch by variant name (often RSID)
pf.get_genotypes(snp='rs1235123')
# fetch by SNP integer index
pf.get_genotypes(snp_index=0)