utilis/README.md

In shanwai1234/GPWAS: Genome-Phenome Wide Association Studies

Determining P-value threshold from GPWAS based on the permutation-based FDR approach

Selecting a p-value based upon FDR to determine your p-value threshold Using the command

Rscript FDR-GPWAS.R real-pvalue.txt merged-permutation-pvalue.txt 5

Note: real-pvalue.txt is the gene p-value output from GPWAS using real phenotype Data; merged-permutation-pvalue.txt is the gene p-value output from GPWAS using permuted phenotype data; 5 changes this to the number of permutation you run.

shanwai1234/GPWAS documentation built on Feb. 16, 2023, 3:15 a.m.