From ba2370f3ffccbaada26db1d04a0c33053ce390ff Mon Sep 17 00:00:00 2001
From: Stefan Kleeberger <stefan.kleeberger@gmail.com>
Date: Mon, 21 Mar 2016 20:38:59 +0100
Subject: [PATCH] unformatted helptext

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 # kleEpistasis
 Brute-force 3-way Interaction calculation for genetic studies
+
+Welcome to kleEpistasis. A tool for performing 3-way genetic interaction analysis.
+
+Contact: stefan.kleeberger@gmail.com (Stefan Kleeberger, Programmer), bmm@psych.mpg.de (Prof. Dr. Bertram Mueller-Myhsok, Supervisor) Max Planck Institute of Psychiatry, Munich, 2015
+		
+In order to perform brute-force statistical 3-way interaction tests on SNP data, you will have to provide your data in PLINK binary format and a Phenotype in PLINK alternate phenotype format. Please see "http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#bed" and "http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#pheno" for more information regarding file formats.
+
+
+
+Flags:
+
+
+REQUIRED
+
+'-path [path]' Absolute or relative path to plink files in binary format (.bed .bim .fam) !>> without <<! file extention
+
+'-pathPheno [path]' Absolute or relative path to plink alternate phenotype file !>> with <<! file extention\
+
+'-outPath [path]' Absolute or relative path to file where results will be written !>> with <<! file extention (.csv)
+
+'-device [0,1,...]' GPU identifier, starting from 0 for first Graphics Card increasing in whole numbers
+
+'-blockSize [2,3,...]' \t parameter for optimizing runtime. See explicit paragraph beneath
+
+'-threads [1,2,...]' \t Number of threads to process results. See explicit paragraph beneath
+
+'-alphaPercent ]0.0;50.0[' \t Significance level for two-sided test. Allowed values: ]0.0;50.0[
+
+
+OPTIONAL
+
+'-pheno [0,1,...]' \t If your Phenotype file contains multiple phenotypes, you can use this flag to specify which phenotype should be used.
+If you skip the '-pheno' flag, the first phenotype will be used (equivalent to '-pheno 0').
+The second phenotype has index 1, the third index 2 and so forth...
+
+'-testBlockSize 1' \t This will start a test-run with only one sub-matrix to be calculated.
+Use this flag to reduce runtime to test for the best possible value for '-blockSize'
+This will not create ANY results!
+
+-blockSize:
+If you are familiar with CUDA, you know what's it about. Otherwise you needn't get too deep into this.
+All you need to know is that this parameter has to be found by trial and error.
+Use the '-testBlockSize 1' to reduce runtime dramatically and try different values for blockSize
+We achived best results with '-blockSize 4' on a NVIDIA Tesla K40
+
+-threads:
+Results will be processed in backroud by the CPU while the GPU creates new results.
+Depending on your CPU und Graphics Card, the GPU has to wait for the CPU to finish befor copying the next results.
+To resolve this the task is split into chuncks and processed by one thread each.
+We used an Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz combined with a NVIDIA Tesla K40 and 8 threads (-threads 8) without encountering wait time.
+This programm will altogether create n+2 threads with n as the number passed via the '-threads' flag.
+
+
+Memory:
+Doing a run on 5k SNPs and 1k Individuals, you need at least 20GB of RAM
+Execution time:
+We were able to perform a run on 5k SNPs and 1k Individuals, on an Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz combined with a NVIDIA Tesla K40 in approx. " 2 hours"
+
+
+Result file:
+The file containing the results has 4 columns: 
+Positio_ SNP1,Positio_ SNP2,Position_SNP3,Calculated_Value
+and as many rows as significant results have been found.
+
+
+Example calls:
+For performing a runtime test:
+./bin/kleEpistasis -path /home/testuser/testdata/plink -pathPheno /home/testuser/testdata/pheno.txt -outPath /home/testuser/results/testDataRes.csv -device 0 -blockSize 4 -threads 8 -alphaPercent 5 -testBlockSize 1
+For performing a complete run:
+./bin/kleEpistasis -path /home/testuser/testdata/plink -pathPheno /home/testuser/testdata/pheno.txt -outPath /home/testuser/results/testDataRes.csv -device 0 -blockSize 4 -threads 8 -alphaPercent 5
+