Python code for MTaSPUsSet

IL-YOUP KWAK ikwak@umn.edu

python code for MTaSPUsSet (Multiple-trait, gene-level adaptive association testing with GWAS summary statistics) test.

Here's a description of the files:

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[MTaSPUsSet.py] - MTaSPUsSet test using python. Need five arguments, Z-score matrix (Zs.txt), correlation matrix among phenotypes (corPhe.txt), correlation matrix among SNPs (corSNP.txt), the number of permutations ( 1000 ) and the file name where result outputs to be saved (out.txt).

[util.py] - some useful python functions used in MTaSPUsSet.py.

[Zs.txt] - example Z score matrix used for MTaSPUsSet.py. (14 rows (#SNPs) and 6 columns (#Phenotypes) )

[corPhe.txt] - example correlation matrix among phenotypes (6 phenotypes, 6 by 6 matrix).

[corSNP.txt] - example correlation matrix among SNPs (14 SNPs, 14 by 14 matrix).

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How to execute :

./MTaSPUsSet.py Zs.txt corPhe.txt corSNP.txt 1000 out.txt 

Results (MTSPUsSet and MTaSPUsSet p-values) are saved in out.txt