PEPIS: A Pipeline for estimating EPIStatic effect in Quantitative Trait Locus Mapping and Genome-Wide Association Studies   
Location:  Analysis

Sub-Pipeline 1. Kinship Matrix Calculation
Step 1.1 Upload Coded Additive Genotypic Data file (a mxn matrix, e.g Z.txt/Z.csv)   [Download demo]    
- upload data size limit: 2G
 
Step 1.2 Upload Coded Domiance Genotypic Data file(a mxn matrix, e.g W.txt/W.csv)  [Download demo]    
- upload data size limit: 2G
 
Step 1.3  Epistatic Effect  Z->W Transition(Z:-1,0,1/W:0,1,0)
 
Sub-Pipeline 2. PolyGenic QTL Mapping Bypass
Step 2.1 Upload Quantative Marker realted Phenotyic File(a nx1 vecotr, e.g phe.txt)  [Download demo]    
-upload data size limit:2G
 
Step 2.2 Polygenic Component Analysis
 
Step 2.3 Main Effect(Additive+Domiance) QTL Mapping Bypass
 
Step 2.4 Epistatic Effect(aa, ad, da, dd) QTL Mapping Bypass


Flowchart of Data Analysis

           

Reminder to the Users:
1. Please carefully check your data file formats before submit: Z and W matrix files must be comma delimited text file, and stored as m(rows, Bins)xn(cols, Individuals), each row corresponds to one SNP/Bin marker; phenotype file must be stored as n rows and each row corresponds to one individual.
2. Welcome to contact us(wezhang AT noble.org) for your speicifc data analysis.
3. Please cite our paper: Zhang W, Dai X, Wang Q, Xu S, Zhao PX (2016) PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies. PLoS Comput Biol 12(5): e1004925. doi:10.1371/journal.pcbi.1004925.