Run a multiple linear regression of one phenotype against one or more phenotypes
This script takes in a tab-delimited clinical traits file from the HMDP database, runs a mutliple regression of one phenotype on one or more other phenotypes, and writes the regression summary of results to a text file and the regression plots to a png file. The file should be preprocessed using preprocess.py from the mouseGWASAnalysisPackage.
Use Python3 is required to use this script. To run the script, simply run the following command. In this example, the file is called preprocessed_clinical_traits_chow2.tsv and the dependent variable from the file is Lean_mass, which is being regressed against the three phenotypes Fat_mass, HDL, and NMR_total_Mass (which should be separated by a space in the command line).
python3 regress_pheno.py --clinical /path/to/my/preprocessed_clinical_traits_chow2.tsv --target Lean_mass --regress Fat_mass HDL NMR_total_Mass
The script will write the summary of OLS results from the mutliple linear regression to a text file regression_summary.txt to the current directory.
The script will save the Residual Plot, QQ Plot, Scale-Location Plot, and Leverage Plot to a png file model_plots.png to the current directory.