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<html>
<body>
<head>
<link rel="stylesheet" href="plink.css" type="text/css">
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=utf-8">
<title>PLINK: Whole genome data analysis toolset</title>
</head>
<!--<html>-->
<!--<title>PLINK</title>-->
<!--<body>-->
<font size="6" color="darkgreen"><b>plink...</b></font>
<div style="position:absolute;right:10px;top:10px;font-size:
75%"><em>Last original <tt>PLINK</tt> release is <b>v1.07</b>
(10-Oct-2009); <b>PLINK 1.9</b> is now <a href="plink2.shtml"> available</a> for beta-testing</em></div>
<h1>Whole genome association analysis toolset</h1>
<font size="1" color="darkgreen">
<em>
<a href="index.shtml">Introduction</a> |
<a href="contact.shtml">Basics</a> |
<a href="download.shtml">Download</a> |
<a href="reference.shtml">Reference</a> |
<a href="data.shtml">Formats</a> |
<a href="dataman.shtml">Data management</a> |
<a href="summary.shtml">Summary stats</a> |
<a href="thresh.shtml">Filters</a> |
<a href="strat.shtml">Stratification</a> |
<a href="ibdibs.shtml">IBS/IBD</a> |
<a href="anal.shtml">Association</a> |
<a href="fanal.shtml">Family-based</a> |
<a href="perm.shtml">Permutation</a> |
<a href="ld.shtml">LD calcualtions</a> |
<a href="haplo.shtml">Haplotypes</a> |
<a href="whap.shtml">Conditional tests</a> |
<a href="proxy.shtml">Proxy association</a> |
<a href="pimputation.shtml">Imputation</a> |
<a href="dosage.shtml">Dosage data</a> |
<a href="metaanal.shtml">Meta-analysis</a> |
<a href="annot.shtml">Result annotation</a> |
<a href="clump.shtml">Clumping</a> |
<a href="grep.shtml">Gene Report</a> |
<a href="epi.shtml">Epistasis</a> |
<a href="cnv.shtml">Rare CNVs</a> |
<a href="gvar.shtml">Common CNPs</a> |
<a href="rfunc.shtml">R-plugins</a> |
<a href="psnp.shtml">SNP annotation</a> |
<a href="simulate.shtml">Simulation</a> |
<a href="profile.shtml">Profiles</a> |
<a href="ids.shtml">ID helper</a> |
<a href="res.shtml">Resources</a> |
<a href="flow.shtml">Flow chart</a> |
<a href="misc.shtml">Misc.</a> |
<a href="faq.shtml">FAQ</a> |
<a href="gplink.shtml">gPLINK</a>
</em></font>
</p>
<table border=0>
<tr>
<td bgcolor="lightblue" valign="top" width=20%>
<font size="1">
<a href="index.shtml">1. Introduction</a> </p>
<a href="contact.shtml">2. Basic information</a> </p>
<ul>
<li> <a href="contact.shtml#cite">Citing PLINK</a>
<li> <a href="contact.shtml#probs">Reporting problems</a>
<li> <a href="news.shtml">What's new?</a>
<li> <a href="pdf.shtml">PDF documentation</a>
</ul>
<a href="download.shtml">3. Download and general notes</a> </p>
<ul>
<li> <a href="download.shtml#download">Stable download</a>
<li> <a href="download.shtml#latest">Development code</a>
<li> <a href="download.shtml#general">General notes</a>
<li> <a href="download.shtml#msdos">MS-DOS notes</a>
<li> <a href="download.shtml#nix">Unix/Linux notes</a>
<li> <a href="download.shtml#compilation">Compilation</a>
<li> <a href="download.shtml#input">Using the command line</a>
<li> <a href="download.shtml#output">Viewing output files</a>
<li> <a href="changelog.shtml">Version history</a>
</ul>
<a href="reference.shtml">4. Command reference table</a> </p>
<ul>
<li> <a href="reference.shtml#options">List of options</a>
<li> <a href="reference.shtml#output">List of output files</a>
<li> <a href="newfeat.shtml">Under development</a>
</ul>
<a href="data.shtml">5. Basic usage/data formats</a>
<ul>
<li> <a href="data.shtml#plink">Running PLINK</a>
<li> <a href="data.shtml#ped">PED files</a>
<li> <a href="data.shtml#map">MAP files</a>
<li> <a href="data.shtml#tr">Transposed filesets</a>
<li> <a href="data.shtml#long">Long-format filesets</a>
<li> <a href="data.shtml#bed">Binary PED files</a>
<li> <a href="data.shtml#pheno">Alternate phenotypes</a>
<li> <a href="data.shtml#covar">Covariate files</a>
<li> <a href="data.shtml#clst">Cluster files</a>
<li> <a href="data.shtml#sets">Set files</a>
</ul>
<a href="dataman.shtml">6. Data management</a> </p>
<ul>
<li> <a href="dataman.shtml#recode">Recode</a>
<li> <a href="dataman.shtml#recode">Reorder</a>
<li> <a href="dataman.shtml#snplist">Write SNP list</a>
<li> <a href="dataman.shtml#updatemap">Update SNP map</a>
<li> <a href="dataman.shtml#updateallele">Update allele information</a>
<li> <a href="dataman.shtml#refallele">Force reference allele</a>
<li> <a href="dataman.shtml#updatefam">Update individuals</a>
<li> <a href="dataman.shtml#wrtcov">Write covariate files</a>
<li> <a href="dataman.shtml#wrtclst">Write cluster files</a>
<li> <a href="dataman.shtml#flip">Flip strand</a>
<li> <a href="dataman.shtml#flipscan">Scan for strand problem</a>
<li> <a href="dataman.shtml#merge">Merge two files</a>
<li> <a href="dataman.shtml#mergelist">Merge multiple files</a>
<li> <a href="dataman.shtml#extract">Extract SNPs</a>
<li> <a href="dataman.shtml#exclude">Remove SNPs</a>
<li> <a href="dataman.shtml#zero">Zero out sets of genotypes</a>
<li> <a href="dataman.shtml#keep">Extract Individuals</a>
<li> <a href="dataman.shtml#remove">Remove Individuals</a>
<li> <a href="dataman.shtml#filter">Filter Individuals</a>
<li> <a href="dataman.shtml#attrib">Attribute filters</a>
<li> <a href="dataman.shtml#makeset">Create a set file</a>
<li> <a href="dataman.shtml#tabset">Tabulate SNPs by sets</a>
<li> <a href="dataman.shtml#snp-qual">SNP quality scores</a>
<li> <a href="dataman.shtml#geno-qual">Genotypic quality scores</a>
</ul>
<a href="summary.shtml">7. Summary stats</a>
<ul>
<li> <a href="summary.shtml#missing">Missingness</a>
<li> <a href="summary.shtml#oblig_missing">Obligatory missingness</a>
<li> <a href="summary.shtml#clustermissing">IBM clustering</a>
<li> <a href="summary.shtml#testmiss">Missingness by phenotype</a>
<li> <a href="summary.shtml#mishap">Missingness by genotype</a>
<li> <a href="summary.shtml#hardy">Hardy-Weinberg</a>
<li> <a href="summary.shtml#freq">Allele frequencies</a>
<li> <a href="summary.shtml#prune">LD-based SNP pruning</a>
<li> <a href="summary.shtml#mendel">Mendel errors</a>
<li> <a href="summary.shtml#sexcheck">Sex check</a>
<li> <a href="summary.shtml#pederr">Pedigree errors</a>
</ul>
<a href="thresh.shtml">8. Inclusion thresholds</a>
<ul>
<li> <a href="thresh.shtml#miss2">Missing/person</a>
<li> <a href="thresh.shtml#maf">Allele frequency</a>
<li> <a href="thresh.shtml#miss1">Missing/SNP</a>
<li> <a href="thresh.shtml#hwd">Hardy-Weinberg</a>
<li> <a href="thresh.shtml#mendel">Mendel errors</a>
</ul>
<a href="strat.shtml">9. Population stratification</a>
<ul>
<li> <a href="strat.shtml#cluster">IBS clustering</a>
<li> <a href="strat.shtml#permtest">Permutation test</a>
<li> <a href="strat.shtml#options">Clustering options</a>
<li> <a href="strat.shtml#matrix">IBS matrix</a>
<li> <a href="strat.shtml#mds">Multidimensional scaling</a>
<li> <a href="strat.shtml#outlier">Outlier detection</a>
</ul>
<a href="ibdibs.shtml">10. IBS/IBD estimation</a>
<ul>
<li> <a href="ibdibs.shtml#genome">Pairwise IBD</a>
<li> <a href="ibdibs.shtml#inbreeding">Inbreeding</a>
<li> <a href="ibdibs.shtml#homo">Runs of homozygosity</a>
<li> <a href="ibdibs.shtml#segments">Shared segments</a>
</ul>
<a href="anal.shtml">11. Association</a>
<ul>
<li> <a href="anal.shtml#cc">Case/control</a>
<li> <a href="anal.shtml#fisher">Fisher's exact</a>
<li> <a href="anal.shtml#model">Full model</a>
<li> <a href="anal.shtml#strat">Stratified analysis</a>
<li> <a href="anal.shtml#homog">Tests of heterogeneity</a>
<li> <a href="anal.shtml#hotel">Hotelling's T(2) test</a>
<li> <a href="anal.shtml#qt">Quantitative trait</a>
<li> <a href="anal.shtml#qtmeans">Quantitative trait means</a>
<li> <a href="anal.shtml#qtgxe">Quantitative trait GxE</a>
<li> <a href="anal.shtml#glm">Linear and logistic models</a>
<li> <a href="anal.shtml#set">Set-based tests</a>
<li> <a href="anal.shtml#adjust">Multiple-test correction</a>
</ul>
<a href="fanal.shtml">12. Family-based association</a>
<ul>
<li> <a href="fanal.shtml#tdt">TDT</a>
<li> <a href="fanal.shtml#ptdt">ParenTDT</a>
<li> <a href="fanal.shtml#poo">Parent-of-origin</a>
<li> <a href="fanal.shtml#dfam">DFAM test</a>
<li> <a href="fanal.shtml#qfam">QFAM test</a>
</ul>
<a href="perm.shtml">13. Permutation procedures</a>
<ul>
<li> <a href="perm.shtml#perm">Basic permutation</a>
<li> <a href="perm.shtml#aperm">Adaptive permutation</a>
<li> <a href="perm.shtml#mperm">max(T) permutation</a>
<li> <a href="perm.shtml#rank">Ranked permutation</a>
<li> <a href="perm.shtml#genedropmodel">Gene-dropping</a>
<li> <a href="perm.shtml#cluster">Within-cluster</a>
<li> <a href="perm.shtml#mkphe">Permuted phenotypes files</a>
</ul>
<a href="ld.shtml">14. LD calculations</a>
<ul>
<li> <a href="ld.shtml#ld1">2 SNP pairwise LD</a>
<li> <a href="ld.shtml#ld2">N SNP pairwise LD</a>
<li> <a href="ld.shtml#tags">Tagging options</a>
<li> <a href="ld.shtml#blox">Haplotype blocks</a>
</ul>
<a href="haplo.shtml">15. Multimarker tests</a>
<ul>
<li> <a href="haplo.shtml#hap1">Imputing haplotypes</a>
<li> <a href="haplo.shtml#precomputed">Precomputed lists</a>
<li> <a href="haplo.shtml#hap2">Haplotype frequencies</a>
<li> <a href="haplo.shtml#hap3">Haplotype-based association</a>
<li> <a href="haplo.shtml#hap3c">Haplotype-based GLM tests</a>
<li> <a href="haplo.shtml#hap3b">Haplotype-based TDT</a>
<li> <a href="haplo.shtml#hap4">Haplotype imputation</a>
<li> <a href="haplo.shtml#hap5">Individual phases</a>
</ul>
<a href="whap.shtml">16. Conditional haplotype tests</a>
<ul>
<li> <a href="whap.shtml#whap1">Basic usage</a>
<li> <a href="whap.shtml#whap2">Specifying type of test</a>
<li> <a href="whap.shtml#whap3">General haplogrouping</a>
<li> <a href="whap.shtml#whap4">Covariates and other SNPs</a>
</ul>
<a href="proxy.shtml">17. Proxy association</a>
<ul>
<li> <a href="proxy.shtml#proxy1">Basic usage</a>
<li> <a href="proxy.shtml#proxy2">Refining a signal</a>
<li> <a href="proxy.shtml#proxy2b">Multiple reference SNPs</a>
<li> <a href="proxy.shtml#proxy3">Haplotype-based SNP tests</a>
</ul>
<a href="pimputation.shtml">18. Imputation (beta)</a>
<ul>
<li> <a href="pimputation.shtml#impute1">Making reference set</a>
<li> <a href="pimputation.shtml#impute2">Basic association test</a>
<li> <a href="pimputation.shtml#impute3">Modifying parameters</a>
<li> <a href="pimputation.shtml#impute4">Imputing discrete calls</a>
<li> <a href="pimputation.shtml#impute5">Verbose output options</a>
</ul>
<a href="dosage.shtml">19. Dosage data</a>
<ul>
<li> <a href="dosage.shtml#format">Input file formats</a>
<li> <a href="dosage.shtml#assoc">Association analysis</a>
<li> <a href="dosage.shtml#output">Outputting dosage data</a>
</ul>
<a href="metaanal.shtml">20. Meta-analysis</a>
<ul>
<li> <a href="metaanal.shtml#basic">Basic usage</a>
<li> <a href="metaanal.shtml#opt">Misc. options</a>
</ul>
<a href="annot.shtml">21. Annotation</a>
<ul>
<li> <a href="annot.shtml#basic">Basic usage</a>
<li> <a href="annot.shtml#opt">Misc. options</a>
</ul>
<a href="clump.shtml">22. LD-based results clumping</a>
<ul>
<li> <a href="clump.shtml#clump1">Basic usage</a>
<li> <a href="clump.shtml#clump2">Verbose reporting</a>
<li> <a href="clump.shtml#clump3">Combining multiple studies</a>
<li> <a href="clump.shtml#clump4">Best single proxy</a>
</ul>
<a href="grep.shtml">23. Gene-based report</a>
<ul>
<li> <a href="grep.shtml#grep1">Basic usage</a>
<li> <a href="grep.shtml#grep2">Other options</a>
</ul>
<a href="epi.shtml">24. Epistasis</a>
<ul>
<li> <a href="epi.shtml#snp">SNP x SNP</a>
<li> <a href="epi.shtml#case">Case-only</a>
<li> <a href="epi.shtml#gene">Gene-based</a>
</ul>
<a href="cnv.shtml">25. Rare CNVs</a>
<ul>
<li> <a href="cnv.shtml#format">File format</a>
<li> <a href="cnv.shtml#maps">MAP file construction</a>
<li> <a href="cnv.shtml#loading">Loading CNVs</a>
<li> <a href="cnv.shtml#olap_check">Check for overlap</a>
<li> <a href="cnv.shtml#type_filter">Filter on type </a>
<li> <a href="cnv.shtml#gene_filter">Filter on genes </a>
<li> <a href="cnv.shtml#freq_filter">Filter on frequency </a>
<li> <a href="cnv.shtml#burden">Burden analysis</a>
<li> <a href="cnv.shtml#burden2">Geneset enrichment</a>
<li> <a href="cnv.shtml#assoc">Mapping loci</a>
<li> <a href="cnv.shtml#reg-assoc">Regional tests</a>
<li> <a href="cnv.shtml#qt-assoc">Quantitative traits</a>
<li> <a href="cnv.shtml#write_cnvlist">Write CNV lists</a>
<li> <a href="cnv.shtml#report">Write gene lists</a>
<li> <a href="cnv.shtml#groups">Grouping CNVs </a>
</ul>
<a href="gvar.shtml">26. Common CNPs</a>
<ul>
<li> <a href="gvar.shtml#cnv2"> CNPs/generic variants</a>
<li> <a href="gvar.shtml#cnv2b"> CNP/SNP association</a>
</ul>
<a href="rfunc.shtml">27. R-plugins</a>
<ul>
<li> <a href="rfunc.shtml#rfunc1">Basic usage</a>
<li> <a href="rfunc.shtml#rfunc2">Defining the R function</a>
<li> <a href="rfunc.shtml#rfunc2b">Example of debugging</a>
<li> <a href="rfunc.shtml#rfunc3">Installing Rserve</a>
</ul>
<a href="psnp.shtml">28. Annotation web-lookup</a>
<ul>
<li> <a href="psnp.shtml#psnp1">Basic SNP annotation</a>
<li> <a href="psnp.shtml#psnp2">Gene-based SNP lookup</a>
<li> <a href="psnp.shtml#psnp3">Annotation sources</a>
</ul>
<a href="simulate.shtml">29. Simulation tools</a>
<ul>
<li> <a href="simulate.shtml#sim1">Basic usage</a>
<li> <a href="simulate.shtml#sim2">Resampling a population</a>
<li> <a href="simulate.shtml#sim3">Quantitative traits</a>
</ul>
<a href="profile.shtml">30. Profile scoring</a>
<ul>
<li> <a href="profile.shtml#prof1">Basic usage</a>
<li> <a href="profile.shtml#prof2">SNP subsets</a>
<li> <a href="profile.shtml#dose">Dosage data</a>
<li> <a href="profile.shtml#prof3">Misc options</a>
</ul>
<a href="ids.shtml">31. ID helper</a>
<ul>
<li> <a href="ids.shtml#ex">Overview/example</a>
<li> <a href="ids.shtml#intro">Basic usage</a>
<li> <a href="ids.shtml#check">Consistency checks</a>
<li> <a href="ids.shtml#alias">Aliases</a>
<li> <a href="ids.shtml#joint">Joint IDs</a>
<li> <a href="ids.shtml#lookup">Lookups</a>
<li> <a href="ids.shtml#replace">Replace values</a>
<li> <a href="ids.shtml#match">Match files</a>
<li> <a href="ids.shtml#qmatch">Quick match files</a>
<li> <a href="ids.shtml#misc">Misc.</a>
</ul>
<a href="res.shtml">32. Resources</a>
<ul>
<li> <a href="res.shtml#hapmap">HapMap (PLINK format)</a>
<li> <a href="res.shtml#teach">Teaching materials</a>
<li> <a href="res.shtml#mmtests">Multimarker tests</a>
<li> <a href="res.shtml#sets">Gene-set lists</a>
<li> <a href="res.shtml#glist">Gene range lists</a>
<li> <a href="res.shtml#attrib">SNP attributes</a>
</ul>
<a href="flow.shtml">33. Flow-chart</a>
<ul>
<li> <a href="flow.shtml">Order of commands</a>
</ul>
<a href="misc.shtml">34. Miscellaneous</a>
<ul>
<li> <a href="misc.shtml#opt">Command options/modifiers</a>
<li> <a href="misc.shtml#output">Association output modifiers</a>
<li> <a href="misc.shtml#species">Different species</a>
<li> <a href="misc.shtml#bugs">Known issues</a>
</ul>
<a href="faq.shtml">35. FAQ & Hints</a>
</p>
<a href="gplink.shtml">36. gPLINK</a>
<ul>
<li> <a href="gplink.shtml">gPLINK mainpage</a>
<li> <a href="gplink_tutorial/index.html">Tour of gPLINK</a>
<li> <a href="gplink.shtml#overview">Overview: using gPLINK</a>
<li> <a href="gplink.shtml#locrem">Local versus remote modes</a>
<li> <a href="gplink.shtml#start">Starting a new project</a>
<li> <a href="gplink.shtml#config">Configuring gPLINK</a>
<li> <a href="gplink.shtml#plink">Initiating PLINK jobs</a>
<li> <a href="gplink.shtml#view">Viewing PLINK output</a>
<li> <a href="gplink.shtml#hv">Integration with Haploview</a>
<li> <a href="gplink.shtml#down">Downloading gPLINK</a></p>
</ul>
</font>
</td><td width=5%>
<td valign="top">
</p>
<h1>Epistasis</h1>
For disease-trait population-based samples, it is possible to test for
epistasis. The epistasis test can either be case-only or
case-control. All pairwise combinations of SNPs can be tested:
although this may or may not be desirable in statistical terms, it is
computationally feasible for moderate datasets using PLINK, e.g. the
4.5 billion two-locus tests generated from a 100K data set took just
over 24 hours to run, for approximately 500 individuals (with
the <tt>--fast-epistasis</tt> command). </p>
Alternatively, sets can be specified (e.g. to test only the most
significant 100 SNPs against all other SNPs, or against themselves,
etc). The output consists only pairwise epistatic results above a
certain significance value; also, for each SNP, a summary of all the
pairwise epistatic tests is given (e.g. maximum test, proportion of
tests significant at a certain threshold, etc).
</p>
To test for gene-by-environment interaction, see either
the <a href="anal.shtml#strat">section on stratified analyses</a> for
disease traits, or the <a href="anal.shtml#qtgxe">section on QTL
GxE</a> for quantitative traits.
</p>
<strong>IMPORTANT!</strong> These tests for epistasis are currently
only applicable for population-based samples, not family-based.
<a name="snp">
<h2>SNP x SNP epistasis</h2>
</a></p>
To test SNP x SNP epistasis for case/control population-based samplse, use the command
<h5>
plink --file mydaya --epistasis
</h5></p>
which will send output to the files
<pre>
plink.epi.cc
plink.epi.cc.summary
</pre>
where <tt>cc</tt> = case-control; for quantitative traits, <tt>cc</tt> will be replaced by <tt>qt</tt>.
</P>
The default test uses either linear or logistic regression, depending on whether the phenoype is
a quantitative or binary trait. PLINK makes a model based on allele dosage for each SNP, <tt>A</tt>
and <tt>B</tt>, and fits the model in the form of
<pre>
Y ~ b0 + b1.A + b2.B + b3.AB + e
</pre>
The test for interaction is based on the coefficient <tt>b3</tt>.
This test therefore only considers allelic by allelic epistasis.
Currently, covariates can not be included when using this
command. Similarly, permutation, and use of modifier commands such
as <tt>--genotypic</tt>, <tt>--within</tt> or <tt>--sex</tt>, etc, are
not currently available.
</p>
<strong>Important</strong> The <tt>--epistasis</tt> command is set up
for testing a potentially very large number of SNP by SNP comparisons,
most of which would not be significant or of interest. Because the output
may contains millions or billions of line, the default is to only output
tests with p-values less than 1e-4, as specified by the <tt>--epi1</tt>
option (see below). If your dataset is much smaller and you definitely
want to see all the output, add <tt>--epi1 1 </tt>. If you do not, odds
are you'll see a blank output file except for the header (i.e. immediately
telling you that none of the tests were significant at 1e-4).
</p><b><font color="green">Specifying which SNPs to test</font></b> </p>
There are different modes for specifying which SNPs are tested:
<pre>ALL x ALL</pre>
<h5>
plink --file mydata --epistasis
</h5></p>
<pre>SET1 x SET1 <em> { where epi.set contains only 1 set }</em></pre>
<h5>
plink --file mydata --epistasis --set-test --set epi.set
</h5></p>
<pre>SET1 x ALL <em> { where epi.set contains only 1 set } </em></pre>
<h5>
plink --file mydata --epistasis --set-test --set epi.set --set-by-all
</h5></p>
<pre>SET1 x SET2 <em> { where epi.set contains 2 sets } </em> </pre>
<h5>
plink --file mydata --epistasis --set-test --set epi.set
</h5></p>
For the 'symmetrical' cases (ALLxALL and SET1xSET1) then only unique pairs
are analysed. </p>
For the other two cases (SET1xALL, SET1xSET2) then all pairs are
analysed (e.g. will perform SNPA x SNPB as well as SNPB x SNPA, if A
and B are in both SET1 and SET2). It will not try to analysis SNPA x
SNPA however.</p>
</p><b><font color="green">The output</font></b> </p>
The output can be controlled via
<h5>
plink --file mydata --epistasis --epi1 0.0001
</h5></p>
which means only record results that are significant p<=0.0001. (This
prevents too much output from being generated). The output is in the form
<pre>
CHR1 Chromosome of first SNP
SNP1 Identifier for first SNP
CHR2 Chromosome of second SNP
SNP2 Identifier for second SNP
OR_INT Odds ratio for interaction
STAT Chi-square statistic, 1df
P Asymptotic p-value
</pre>
The odds ratio for interaction is interpreted in the standard manner:
a value of 1.0 indicates no effect. To better visualise the manner of
an interaction, use the <tt>--twolocus</tt> command to produce a
report. For example:
<h5>
plink --bfile mydata --twolocus rs9442385 rs4486391
</h5></p>
generates the file
<pre>
plink.twolocus
</pre>
which contains counts and frequencies of the two locus genotypes,
e.g. (there is no interaction evident in this case):
<pre>
All individuals
===============
rs4486391
1/1 1/4 4/4 0/0 */*
rs9442385 4/4 4 5 7 1 17
4/3 7 15 14 0 36
3/3 6 20 10 0 36
0/0 0 1 0 0 1
*/* 17 41 31 1 90
rs4486391
1/1 1/4 4/4 0/0 */*
rs9442385 4/4 0.044 0.056 0.078 0.011 0.189
4/3 0.078 0.167 0.156 0.000 0.400
3/3 0.067 0.222 0.111 0.000 0.400
0/0 0.000 0.011 0.000 0.000 0.011
*/* 0.189 0.456 0.344 0.011 1.000
</pre>
For case/control data, two similar sets of tables are included which
stratify the two-locus genotype counts by cases and controls
</p>
A second part of the output: for each SNP in SET1, or in ALL if no
sets were specified, is information about the number of significant
epistatic tests that SNP featured in (i.e. either with ALL other SNPs,
with SET1, or with SET2). The threshold <tt>--epi2</tt> determines this:
<h5>
plink --file mydata --epistasis --epi1 0.0001 --epi2 0.05
</h5></p>
The output in the <tt>plink.epi.cc.summary</tt> file containts the following fields:
<pre>
CHR Chromosome
SNP SNP identifier
N_SIG # significant epistatic tests (p <= "--epi2" threshold)
N_TOT # of valid tests (i.e. non-zero allele counts, etc)
PROP Proportion significant of valid tests
BEST_CHISQ Highest statistic for this SNP
BEST_CHR Chromosome of best SNP
BEST_SNP SNP identifier of best SNP
</pre>
This file should be interpreted as giving only a very rough idea about
the extent of epistasis and which SNPs seem to be interacting
(although, of course, this is a naive statistic as we do not take LD
into account -- i.e. <tt>PROP</tt> does not represent the number
of <em>independent</em> epistatic results). </p>
<h6>A faster epistasis option</h6>
For disease traits only, an approximate but faster method can be used
to screen for epistasis: use the <tt>--fast-epistasis</tt> command
instead of <tt>--epistasis</tt>. This test is based on a Z-score for
difference in SNP1-SNP2 assocation (odds ratio) between cases and
controls (or in cases only, in a case-only analysis). For more
details, see <a href="epidetails.shtml">this page</a>.
</p>
<a name="case">
<h2>Case-only epistasis</h2>
</a></p>
For case-only epistatic analysis,
<h5>
plink --file mydata --fast-epistasis --case-only
</h5></p>
sends output to (<tt>co</tt> = case-only)
<pre>
plink.epi.co
plink.epi.co.summary
</pre>
All other options are as described above.
</p>
Currently, in case-only analysis, only SNPs that are more than 1 Mb
apart, or on different chromosomes, are included in case-only
tests. This behavior can be changed with the <tt>--gap</tt> option,
with the distance specified kb: for example, to specify a gap of 5 Mb,
<h5>
plink --file mydata --fast-epistasis --case-only --gap 5000
</h5></p>
This option is important, as the case-only test for epistasis assumes
that the two SNPs are in linkage equilibrium in the general
population.
<a name="gene">
<h2>Gene-based tests of epistasis</h2>
</a></p>
</p><strong>WARNING</strong> This test is still under heavy
development and not ready for use.
<!--
</p>
For disease traits, in population-based samples, a gene-based
test is available with the <tt>--genepi</tt> option, that
requires a set-file (<tt>--set <em>filename</em></tt>) to
be specified, containing at least two sets/genes
(i.e. specifying the SNPs in two or more genes; the analysis is
pairwise between pairs of genes, not pairs of SNPs).
<h5>
plink --file mydata --genepi --set gene.set
</h5></p>
sends output to
<pre>
plink.genepi
</pre>
If used in conjunction with the <tt>--mperm N</tt> option (currently
only a fixed number of permutations is possible), a file with
empircal p-values will be generated:
<pre>
plink.genepi.mperm
</pre>
It is also possible to specify a <tt>--case-only</tt> analysis with
this option.</p>
</p><strong>WARNING</strong> This test is still under heavy
development and should not be used yet (as of version 0.99j).
</p>
-->
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This document last modified Wednesday, 25-Jan-2017 11:39:26 EST
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