GWAMA(1)
NAME
GWAMA - Genome-Wide Association Meta Analysis
SYNOPSIS
GWAMA [options]
DESCRIPTION
GWAMA (Genome-Wide Association Meta Analysis) software performs meta- analysis of the results of GWA studies of binary or quantitative phenotypes. Fixed- and random-effect meta-analyses are performed for both directly genotyped and imputed SNPs using estimates of the allelic odds ratio and 95% confidence interval for binary traits, and estimates of the allelic effect size and standard error for quantitative phenotypes. GWAMA can be used for analysing the results of all different genetic models (multiplicative, additive, dominant, recessive). The software incorporates error trapping facilities to identify strand alignment errors and allele flipping, and performs tests of heterogeneity of effects between studies.
OPTIONS
-i, --filelist=filename
Specify studies' result files. Default = gwama.in
-o, --output=fileroot
Specify file root for output of analysis. Default = gwama
(gwama.out, gwama.gc.out)
-r, --random
Use random effect correction. Default = disabled
-gc, --genomic_control
Use genomic control for adjusting studies' result files. Default
= disabled
-gco, --genomic_control_output
Use genomic control on meta-analysis summary (i.e. results of
meta- analysis are corrected for gc). Default = disabled
-qt, --quantitative
Select quantitative trait version (BETA and SE columns). Default
= binary trait
-m, --map=filename
Select file name for marker map.
-t, --threshold=0-1
The p-value threshold for showing direction in summary effect
directions. Default = 1
--no_alleles
No allele information has been given. Expecting always the same
EA.
--indel_alleles
Allele labes might contain more than single letter. No strand
checks.
--sex Run gender-differentiated and gender- heterogeneity analysis
(method described in paper Magi, Lindgren & Morris 2010). Gender
info must be provided in filelist file. (second column after
file names is either M or F).
--filter
Set a filtering based on column header. It needs 3 arguments:
column name, equation [>,<,>=,<=,==,!=], filter value. Multiple
filters can be set.
--name_marker
Alternative header to marker name col.
--name_strand
Alternative header to strand column.
--name_n
Alternative header to sample size col.
--name_ea
Alternative header to effect allele column.
--name_nea
Alternative header to non-effect allele column.
--name_eaf
Alternative header to effect allele frequency column.
--name_beta
Alternative header to beta column.
--name_se
Alternative header to std. err. col.
--name_or
Alternative header to OR column.
--name_or_95l
Alternative header to OR 95L column.
--name_or_95u
Alternative header to OR 95U column.
-h, --help
Print this help.
-v, --version
Print GWAMA version number. This manual page must be
insufficient. Please use the help option for a quick reminder of
the options of gwama or turn to its home page with the online
documentation or the downloadable manual.
SEE ALSO
http://www.geenivaramu.ee/en/tools/gwama
AUTHOR
GWAMA was written by Reedik Magi and Andrew P Morris.
Opportunity
Personal Opportunity - Free software gives you access to billions of dollars of software at no cost. Use this software for your business, personal use or to develop a profitable skill. Access to source code provides access to a level of capabilities/information that companies protect though copyrights. Open source is a core component of the Internet and it is available to you. Leverage the billions of dollars in resources and capabilities to build a career, establish a business or change the world. The potential is endless for those who understand the opportunity.
Business Opportunity - Goldman Sachs, IBM and countless large corporations are leveraging open source to reduce costs, develop products and increase their bottom lines. Learn what these companies know about open source and how open source can give you the advantage.
Free Software
Free Software provides computer programs and capabilities at no cost but more importantly, it provides the freedom to run, edit, contribute to, and share the software. The importance of free software is a matter of access, not price. Software at no cost is a benefit but ownership rights to the software and source code is far more significant.
Free Office Software - The Libre Office suite provides top desktop productivity tools for free. This includes, a word processor, spreadsheet, presentation engine, drawing and flowcharting, database and math applications. Libre Office is available for Linux or Windows.
Free Books
The Free Books Library is a collection of thousands of the most popular public domain books in an online readable format. The collection includes great classical literature and more recent works where the U.S. copyright has expired. These books are yours to read and use without restrictions.
Source Code - Want to change a program or know how it works? Open Source provides the source code for its programs so that anyone can use, modify or learn how to write those programs themselves. Visit the GNU source code repositories to download the source.
Education
Study at Harvard, Stanford or MIT - Open edX provides free online courses from Harvard, MIT, Columbia, UC Berkeley and other top Universities. Hundreds of courses for almost all major subjects and course levels. Open edx also offers some paid courses and selected certifications.
Linux Manual Pages - A man or manual page is a form of software documentation found on Linux/Unix operating systems. Topics covered include computer programs (including library and system calls), formal standards and conventions, and even abstract concepts.
