🧬 MaSK-LMM: Matrix-Sketching Linear Mixed Model

We leverage matrix sketching to develop a fast and efficient LMM method called Matrix-Sketching LMM (MaSk-LMM) by sketching the genotype matrix to reduce its dimensions and speed up computations.

Built With

Getting Started

Installing MaSK-LMM

pip install masklmm

Running MaSK-LMM

# Data

data_path = "../sample-data/bn"
bed_fn = data_path+".bed"
pheno_fn = data_path+".phen_w_header"
cov_fn = data_path+".cov_w_header"
pruned_bed_fn = "../sample-data/bn.bed"

# Parameters

maxiters = 10
sample_sketch_size = 0.5
marker_sketch_size = 0.5
block_size = 10000

# MaSkLMM pacakge

from masklmm import MaSkLMM

# Running MaSkLMM

newton = MaSkLMM.compute(bed_fn,
                        pruned_bed_fn,
                        pheno_fn,
                        cov_fn,
                        sample_sketch_size = sample_sketch_size,
                        marker_sketch_size = marker_sketch_size,
                        maxiters = maxiters,
                        block_size = block_size)

# Association results stored in tab-delimited file "masklmm-output"

Authors

Contributors and contact info:

• Myson Burch (myson dot burch at ibm dot com)

• Aritra Bose (a dot bose at ibm dot com)

Version History

• 0.1.0

  • Initial Release