Work on large-scale ML for gene expression prediction based on genotype only.
This project aims to provide a machine-learning based tool for assessing gene expression based on genotype data only.
This tool requires the installation of R software.
No specific dependency, except basic R packages installed by default.
After cloning the repository, you may want to call the get_prediction.R function on a test sample data, to make sure that everything runs properly.
First, move in the src repository, cd <github-clone-location>/src.
Then run predictions for sample data: Rscript get_prediction.R ../test/sample.txt ../test/test_output.txt.
This function takes as inputs:
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- genotype matrix with 0 --> 2 allele count values for individuals (rows) and SNPs (columns).
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- path to output file where estimated gene expression will be stored.
It should create a new file in the test repository, called test_output.txt.