MEGASOFT (c++)

Table of Content

• About
• How to Use
• Prerequisite
• Compile (windows, linux)
• Reference

About

MEGASOFT is a next-level software of METASOFT. In Genome-wide association Study Analysis(GWAS), METASOFT is considered a widely used software, which is effective in performing wide range of basic and complicated meta-analytic methods. However, in terms of scalability, METASOFT lack of memory efficiency as well as computing performance. MEGASOFT is an improved version of METASOFT refered as MEGASOFT where load balancing is used to improve computing performance as well as memory efficiency.

METASOFT mirror Link

How to Use MEGASOFT

METASOFT Overview Link

mirror Link

User's MEGASOFT Guide

MEGASOFT_WIN64.exe -input [inputMS.txt] [option1] [option2] ...
MEGASOFT_LINUX.o -input [inputMS.txt] [option1] [option2] ...

-input <FILE>                       Input file (Required)

-output <FILE>                      Output file (default='out')

-log <FILE>                         Log file (default='log')

-pvalue_table <FILE>                Pvalue table file (default='HanEskinPvalueTable.txt')

-lambda_mean <FLOAT>                (Random Effects) User-specified lambda for mean effect part(default=1.0)

-lambda_hetero <FLOAT>              (Random Effects) User-specified lambda for heterogeneity part (default=1.0)

-binary_effects                     Compute binary effects model p-value (default=false)

-binary_effects_sample <INT>        (Binary effects) Number of importance sampling samples(default=1,000)

-binary_effects_p_thres <FLOAT>     (Binary effects) P-value threshold determining if we will use large number of samples (default=1E-4)

-binary_effects_large <INT>         (Binary effects) Large number of importance sampling samples for p-values above threshold (default=100,000)

-mvalue                             Compute m-value (default=false)

-mvalue_method <METHOD_NAME>        Which method to use to calculate m-value between 'exact' and 'mcmc' (default=exact)

-mvalue_p_thres <FLOAT>             Compute m-values only for SNPs whose FE or RE2 p-value is below this threshold (default=1E-7)

-mvalue_prior_alpha <ALPHA>         Alpha value for Beta dist  prior Betadist(alpha,beta) for existence of effect (default=1.0)

-mvalue_prior_beta <BETA>           Beta value for Beta dist  prior Betadist(alpha,beta) for existence of effect(default=1.0,1.0)

-mvalue_prior_sigma <FLOAT>         Sigma value for normal  prior N(0, sigma^2) for effect(default=0.2)

-mcmc_sample <INT>                  (MCMC) Number of samples  (default=10,000)

-mcmc_burnin <INT>                  (MCMC) Number of burn-in  (default=1,000)

-mcmc_max_num_flip <INT or FLOAT>   (MCMC) Usual move is  flipping N bits where N ~ U(1,max_num_flip). If an integer value i >= 1 is given, max_num_flip = i. If a float value 0 < k < 1 is given, max_num_flip = k * #studies. (default=0.1)

-mcmc_prob_random_move <FLOAT>      (MCMC) Probability that a complete randomization move is suggested (default=0.01)

-seed <INT>                         Random number generator seed (default=0)

-thread <INT>                       Number of thread to use(default=1)

-verbose                            Print RSID verbosely per every 1,000 SNPs (default=false)

-help                               Print help

Prerequisite

In order to Improve and Edit MEGASOFT, boost library is required.

Windows                             boost-x64 1.72.0
Linux                               boost-x64 1.72.0

How to Compile MEGASOFT

Boost Download link

Windows x64 - using Visual Studio 2019(v142)

1. boostrap.bat

2. b2 variant=debug,release link=static threading=multi address-model=64 runtime-link=static -j4 install --prefix=stage

3. Project Properties Page -> Configuration Properties -> VC++ Directories -> Include Directories

   ADD YOUR_BOOST_DIR 
   ..\boost_1_72_0\stage\include\boost-1_72\
   

4. Project Properties Page -> Configuration Properties -> C/C++ -> Code Generation -> Runtime Library

   Set to "Multi-threaded(/MT)"
   

5. Project Properties Page -> Configuration Properties -> Linker -> General -> Additional Library Directories

   ADD 
   YOUR_BOOST_LIB_DIR ..\boost_1_72_0\stage\lib\
   

6. Project Properties Page -> Configuration Properties -> Linker -> Input -> Additional Dependencies

   ADD
   libboost_program_options-vc142-mt-s-x64-1_72.lib
   libboost_thread-vc142-mt-s-x64-1_72.lib
   libboost_system-vc142-mt-s-x64-1_72.lib
   

Linux - using MinGW(g++)

1. boostrap.sh

2. b2 link=static

3. export BOOST_ROOT=/home/user/Desktop/boost_1_72_0
   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$BOOST_ROOT/stage/lib
   

4. Final Compile using g++

   sudo g++ -pthread -I BOOST_ROOT MetaSnp.cpp  MetaSnp.h MetaSoft.cpp LD_LIBRARY_PATH/libboost_thread.a LD_LIBRARY_PATH/libboost_program_options.a LD_LIBRARY_PATH/libboost_system.a -o out.o -g3 -static
   

Reference

• METASOFT
• METASOFT mirror Link
• Boost