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<html>
<title>PLINK</title>
<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>Common copy number polymorphism (CNP) data</h1>
This page describes some basic file formats, convenience functions and
analysis options for common copy number polymorphism (CNP)
data. Support for rare copy number variant (CNV) data is
described <a href="cnv.shtml">here</a>.
</p>
Common copy number variation is represented for specific SNP
genotypes, for example, allowing <tt>A</tt>, <tt>AAB</tt>
or <tt>AABB</tt> calls (being copy number 1,3 and 4 respectively) as
well as the canonical <tt>AA</tt>, <tt>AB</tt> and <tt>BB</tt>
genotypes. These formats are specified via the "generic variant"
(<tt>--gfile</tt>) option.
</p>
Here we assume that some other software package such as
the <a href="http://www.broad.mit.edu/mpg/birdsuite/">Birdsuite</a>
package has previously been used to make calls for either specific
copy-number variable genotypes or to identify particular genomic
regions in individuals that are deletions or duplications, based on
the raw data. That is, PLINK only offers functions for downstream
analysis of CNV data, not for identifying CNVs in the first place,
i.e. similar to the distinction between SNP genotype calling versus
the subsequent analysis of those calls.
</p>
<a name="cnv2">
<h2>Format for common CNVs (generic variant format)</h2>
</a></p>
For common CNVs, that might also have meaningful allelic/SNP
variation, it can be desirable to represent and analyse these not as
segments. The rest of the page considers non-segmental specification
of CNVs: that is, copy-number variable specific genotype calls, such
as <tt>A</tt> or <tt>AAB</tt>.
</p>
Such data are represented with the <em>generic variant</em> file format,
and read into PLINK with the command:
<h5>
plink --gfile mydata
</h5></p>
where three files are assumed to exist
<pre>
mydata.fam (describes individuals, as usual)
mydata.map (describes variants, as usual)
mydaya.gvar (new file format)
</pre>
The <tt>.gvar</tt> file is in long-format: always with 7 fields, one
row per genotype (note that the reference to the first and second
parents above does not imply that paternal or maternal origin should
be known or is used)
<pre>
FID Family ID
IID Individual ID (i.e. person should appear in .fam file)
NAME Variant name (should appear in .map file)
ALLELE1 Code for allele from first parent
DOSAGE1 Copy number for first allele
ALLELE2 Code for allele from second parent
DOSAGE2 Copy number for second allele
</pre>
Some example of using this format to represent different genotypes are shown here:
<pre>
1 1 var1 A 1 C 1 -> normal het
1 1 var2 A 2 C 1 -> AAC genotype
1 1 var3 0 1 0 1 -> missing individual
1 1 var4 0 0 0 0 -> homozygous deletion
1 1 var5 4 1 7 1 -> e.g. 4/7 genotype
2 1 var5 4 1 8 1 -> e.g. 4/8 genotype
1 1 var6 A 0.95 C 1.05 -> expected allele dosage (e.g. from imputation)
</pre>
As currently implemented, all the codings below would be equivalent,
i.e. specifying an <tt>AA</tt> homozygote:
<pre>
1 1 var7 A 1 A 1
2 1 var7 A 0 A 2
3 1 var7 A 2 A 0
4 1 var7 X 0 A 2
5 1 var7 0 0 A 2
</pre>
That is, for a missing (null) genotype, <tt>ALLELE1</tt>
and <tt>ALLELE2</tt> should both be set to 0, and by
convention, <tt>DOSAGE1</tt> and <tt>DOSAGE2</tt> should be 1
(indicating a <tt>0 0</tt> genotype). But if a <tt>DOSAGE</tt> value
is 0, then the value of the corresponding <tt>ALLELE</tt> column does
not matter. Thus, genotypes can have <tt>DOSAGE >= 1</tt> for one
allele, and <tt>DOSAGE</tt> for the other allele: <tt>A 0 B 3</tt>
means 3 copies of allele B and no copies of A; <tt>X 0 B 3</tt> means
the same thing because the <tt>X</tt> is ignored when <tt>DOSAGE=0</tt>.
</p>
When loading this kind of file, <tt>PLINK</tt> will parse allelic and
copy number variation; currently by default it looks for integer
dosage calls in this part of the process. There are currently no
functions implemented yet for fractional counts, but the datatype
exists.
</p>
Alleles and CNVs are then appropriately counted. <tt>PLINK</tt>
assesses and records for each variant whether there is allelic and/or
copy number variation, and this influences downstream analysis.
Currently variation is defined as at least one individual varying, but
in the future thresholds will be added (e.g. to treat a site of a CNV
only if, say, 1% of all individuals have a non-canonical copy number).
</p>
The basic summary output is also in "long format": in the future this
will be expanded and reformated, e.g. to include specific allelic/CNV
frequncies or counts; stratification by phenotype, etc. This summary file
is called
<pre>
plink.gvar.summary
</pre>
and always contains three columns, as illustrated here
<pre>
NAME FIELD VALUE
var1 CHR 1
var1 BP 1
var1 CNV yes
var1 ALLELIC yes
var1 GCOUNT 1000
var1 B 0.6031
var1 A 0.3969
var1 [2] 0.56
var1 [3] 0.378
var1 [4] 0.062
var1 B/B 30:38
var1 BB/B 66:60
var1 BB/BB 42:20
var1 A/B 142:101
var1 A/BB 161:91
var1 A/A 162:87
</pre>
The CN counts are always in [x] to distingush from allele codes, if
they are also numeric. e.g. in this example, 37.5% of sample have the
deletion for example. There can be more than 2 CN states for a given
variant.
</p>
If the trait is binary, then the counts for copy-number specific
genotypes (e.g. <tt>A/BB</tt>) will be given separately for cases and
controls, separated by a colon.
<a name="cnv2b">
<h2>Association models for combined SNP and common CNV data</h2>
</a></p>
<tt>PLINK</tt> has implemented the following regression models
(logistic or linear) currently applicable to biallelic SNPs residing
within CNPs:
<pre>
Y ~ b0 + b1.(A+B) + b2.(A-B)
</pre>
When an association test is performed, extra lines will be appended to the <tt>plink.gvar.summary</tt> file
<pre>
var1 B(SNP) -0.05955
var1 P(SNP) 0.09085
var1 B(CNP) 0.09314
var1 P(CNP) 0.3809
var1 B(CNP|SNP) 0.5638
var1 P(CNP|SNP) 0.0006768
var1 B(SNP|CNP) -0.2042
var1 P(SNP|CNP) 0.0002242
var1 P(SNP&CNP) 0.0007413
</pre>
Covariates can be added with <tt>--covar</tt> as with <tt>--linear</tt> or <tt>--logistic</tt>. The coefficients and
p-values for the SNP and CNP will reflect this, although the specific coefficients and p-values for the covariates
themselves are not shown in the output.
</p>
<b><em>This section is not finished -- more details will be added online presently. </em></b>
</td>
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This document last modified Wednesday, 25-Jan-2017 11:39:26 EST
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