http://statgen.us/index.php?action=history&feed=atom&title=Regression_Exercise 2026-04-05T18:25:18Z Revision history for this page on the wiki MediaWiki 1.26.2 http://statgen.us/index.php?title=Regression_Exercise&diff=271&oldid=prev 2017-03-08T03:30:52Z

<p>‎<span dir="auto"><span class="autocomment">Regression exercise</span></span></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;' lang='en'> <td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 03:30, 8 March 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4" >Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>&#160; load(&quot;dbp.R&quot;)</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>&#160; load(&quot;dbp.R&quot;)</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&#160; ls()<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>dbp[1:5,]<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>result.snp12 = glm (affection ~ rs1112, family=binomial(&quot;logit&quot;), data=dbp)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>print (result.snp12)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>print ( class (result.snp12) )<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>print ( summary(result.snp12) )<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>dev.geno = anova (result.snp12, test=&quot;Chi&quot;)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>lrt.pvalue = pchisq(dev.geno[dim(dev.geno)[1],&quot;Deviance&quot;],<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt; </del>df=2, ncp=0, FALSE)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>print ( lrt.pvalue )<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>print ( summary(result.snp12)$coefficients )<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>snp.beta = summary(result.snp12)$coefficients[2:3,1]<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>print ( snp.beta )<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>print ( exp(snp.beta) )<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>ci = confint (result.snp12)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>print (ci)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>print ( exp(ci) )<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>snp.data = dbp[,c(&quot;affection&quot;, &quot;rs1112&quot;)]<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>snp.data[,&quot;rs1112&quot;] &lt;- as.numeric(snp.data[,&quot;rs1112&quot;]) - 1&lt;br /&gt;summary(snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>result.all = glm (affection ~ rs1112, family=binomial(&quot;logit&quot;),<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt; </del>data=snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>dev.all = anova (result.all, test=&quot;Chi&quot;)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(result.all)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>print(dev.all)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>snp.data = dbp[,c(&quot;affection&quot;, &quot;trait&quot;,&quot;sex&quot;, &quot;age&quot;, &quot;rs1112&quot;, &quot;rs1117&quot;)]<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>snp.data[,&quot;rs1112&quot;] &lt;- as.numeric(snp.data[,&quot;rs1112&quot;]) - 1&lt;br /&gt;snp.data[,&quot;rs1117&quot;] &lt;- as.numeric(snp.data[,&quot;rs1117&quot;]) - 1</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&#160; ls()</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&#160; #<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>result.adj = glm (affection ~ sex + rs1112 , family=binomial(&quot;logit&quot;),<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt; </del>data=snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(result.adj)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>result.adj = glm (affection ~ age + rs1112 , family=binomial(&quot;logit&quot;),<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt; </del>data=snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(result.adj)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>result.adj = glm (affection ~ sex + age + rs1112, family=binomial(&quot;logit&quot;),<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt; </del>data=snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(result.adj)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>result.adj = glm (affection ~ rs1117 + rs1112, family=binomial(&quot;logit&quot;),<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt; </del>data=snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(result.adj)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>anova (result.adj, test=&quot;Chi&quot;)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>result.adj = glm (affection ~ rs1112 + rs1117, family=binomial(&quot;logit&quot;),<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt; </del>data=snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(result.adj)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>anova (result.adj, test=&quot;Chi&quot;)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>result.adj = lm (trait ~ rs1112, data=snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(result.adj)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>result.adj = lm (trait ~ sex + rs1112, data=snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(result.adj)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>result.inter = glm (affection ~ sex * rs1112, family=binomial(&quot;logit&quot;),<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt; </del>data=snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(result.inter)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>result.inter = glm (affection ~ age * rs1112, family=binomial(&quot;logit&quot;),<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt; </del>data=snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(result.inter)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>result.inter = glm (affection ~ rs1112 * rs1117, family=binomial(&quot;logit&quot;),<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt; </del>data=snp.data)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>summary(result.inter)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>#<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>q()</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>dbp[1:5,]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>result.snp12 = glm (affection ~ rs1112, family=binomial(&quot;logit&quot;), data=dbp)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>print (result.snp12)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>print ( class (result.snp12) )</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>print ( summary(result.snp12) )</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>dev.geno = anova (result.snp12, test=&quot;Chi&quot;)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>lrt.pvalue = pchisq(dev.geno[dim(dev.geno)[1],&quot;Deviance&quot;], df=2, ncp=0, FALSE)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>print ( lrt.pvalue )</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>print ( summary(result.snp12)$coefficients )</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>snp.beta = summary(result.snp12)$coefficients[2:3,1]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>print ( snp.beta )</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>print ( exp(snp.beta) )</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>ci = confint (result.snp12)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>print (ci)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>print ( exp(ci) )</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>snp.data = dbp[,c(&quot;affection&quot;, &quot;rs1112&quot;)]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>snp.data[,&quot;rs1112&quot;] &lt;- as.numeric(snp.data[,&quot;rs1112&quot;]) - 1&lt;br /&gt;summary(snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>result.all = glm (affection ~ rs1112, family=binomial(&quot;logit&quot;), data=snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>dev.all = anova (result.all, test=&quot;Chi&quot;)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(result.all)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>print(dev.all)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>snp.data = dbp[,c(&quot;affection&quot;, &quot;trait&quot;,&quot;sex&quot;, &quot;age&quot;, &quot;rs1112&quot;, &quot;rs1117&quot;)]</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>snp.data[,&quot;rs1112&quot;] &lt;- as.numeric(snp.data[,&quot;rs1112&quot;]) - 1&lt;br /&gt;snp.data[,&quot;rs1117&quot;] &lt;- as.numeric(snp.data[,&quot;rs1117&quot;]) - 1</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&#160; #</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>result.adj = glm (affection ~ sex + rs1112 , family=binomial(&quot;logit&quot;), data=snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(result.adj)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>result.adj = glm (affection ~ age + rs1112 , family=binomial(&quot;logit&quot;), data=snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(result.adj)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>result.adj = glm (affection ~ sex + age + rs1112, family=binomial(&quot;logit&quot;), data=snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(result.adj)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>result.adj = glm (affection ~ rs1117 + rs1112, family=binomial(&quot;logit&quot;), data=snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(result.adj)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>anova (result.adj, test=&quot;Chi&quot;)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>result.adj = glm (affection ~ rs1112 + rs1117, family=binomial(&quot;logit&quot;), data=snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(result.adj)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>anova (result.adj, test=&quot;Chi&quot;)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>result.adj = lm (trait ~ rs1112, data=snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(result.adj)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>result.adj = lm (trait ~ sex + rs1112, data=snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(result.adj)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>result.inter = glm (affection ~ sex * rs1112, family=binomial(&quot;logit&quot;), data=snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(result.inter)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>result.inter = glm (affection ~ age * rs1112, family=binomial(&quot;logit&quot;), data=snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(result.inter)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>result.inter = glm (affection ~ rs1112 * rs1117, family=binomial(&quot;logit&quot;), data=snp.data)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>summary(result.inter)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>#</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>q()</div></td></tr> </table>

Serveradmin http://statgen.us/index.php?title=Regression_Exercise&diff=270&oldid=prev 2017-03-08T03:26:46Z

<p>‎<span dir="auto"><span class="autocomment">Regression exercise</span></span></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;' lang='en'> <td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 03:26, 8 March 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l3" >Line 3:</td> <td colspan="2" class="diff-lineno">Line 3:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>In R:</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>In R:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>&#160; load(&quot;dbp.R&quot;)<del class="diffchange diffchange-inline">&lt;br data-attributes=&quot;%20/&quot; /&gt;</del>ls()&lt;br data-attributes=&quot;%20/&quot; /&gt;dbp[1:5,]&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.snp12 = glm (affection ~ rs1112, family=binomial(&quot;logit&quot;), data=dbp)&lt;br data-attributes=&quot;%20/&quot; /&gt;print (result.snp12)&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( class (result.snp12) )&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( summary(result.snp12) )&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;dev.geno = anova (result.snp12, test=&quot;Chi&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;lrt.pvalue = pchisq(dev.geno[dim(dev.geno)[1],&quot;Deviance&quot;],&lt;br data-attributes=&quot;%20/&quot; /&gt; df=2, ncp=0, FALSE)&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( lrt.pvalue )&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( summary(result.snp12)$coefficients )&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.beta = summary(result.snp12)$coefficients[2:3,1]&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( snp.beta )&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( exp(snp.beta) )&lt;br data-attributes=&quot;%20/&quot; /&gt;ci = confint (result.snp12)&lt;br data-attributes=&quot;%20/&quot; /&gt;print (ci)&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( exp(ci) )&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.data = dbp[,c(&quot;affection&quot;, &quot;rs1112&quot;)]&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.data[,&quot;rs1112&quot;]&lt;br /&gt;summary(snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.all = glm (affection ~ rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;dev.all = anova (result.all, test=&quot;Chi&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.all)&lt;br data-attributes=&quot;%20/&quot; /&gt;print(dev.all)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.data = dbp[,c(&quot;affection&quot;, &quot;trait&quot;,&quot;sex&quot;, &quot;age&quot;, &quot;rs1112&quot;, &quot;rs1117&quot;)]&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.data[,&quot;rs1112&quot;]&lt;br /&gt;snp.data[,&quot;rs1117&quot;] &#160;</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>&#160; load(&quot;dbp.R&quot;)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline"> </ins>ls()&lt;br data-attributes=&quot;%20/&quot; /&gt;dbp[1:5,]&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.snp12 = glm (affection ~ rs1112, family=binomial(&quot;logit&quot;), data=dbp)&lt;br data-attributes=&quot;%20/&quot; /&gt;print (result.snp12)&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( class (result.snp12) )&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( summary(result.snp12) )&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;dev.geno = anova (result.snp12, test=&quot;Chi&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;lrt.pvalue = pchisq(dev.geno[dim(dev.geno)[1],&quot;Deviance&quot;],&lt;br data-attributes=&quot;%20/&quot; /&gt; df=2, ncp=0, FALSE)&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( lrt.pvalue )&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( summary(result.snp12)$coefficients )&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.beta = summary(result.snp12)$coefficients[2:3,1]&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( snp.beta )&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( exp(snp.beta) )&lt;br data-attributes=&quot;%20/&quot; /&gt;ci = confint (result.snp12)&lt;br data-attributes=&quot;%20/&quot; /&gt;print (ci)&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( exp(ci) )&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.data = dbp[,c(&quot;affection&quot;, &quot;rs1112&quot;)]&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.data[,&quot;rs1112&quot;] <ins class="diffchange diffchange-inline">&lt;- as.numeric(snp.data[,&quot;rs1112&quot;]) - 1</ins>&lt;br /&gt;summary(snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.all = glm (affection ~ rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;dev.all = anova (result.all, test=&quot;Chi&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.all)&lt;br data-attributes=&quot;%20/&quot; /&gt;print(dev.all)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.data = dbp[,c(&quot;affection&quot;, &quot;trait&quot;,&quot;sex&quot;, &quot;age&quot;, &quot;rs1112&quot;, &quot;rs1117&quot;)]&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.data[,&quot;rs1112&quot;] <ins class="diffchange diffchange-inline">&lt;- as.numeric(snp.data[,&quot;rs1112&quot;]) - 1</ins>&lt;br /&gt;snp.data[,&quot;rs1117&quot;] <ins class="diffchange diffchange-inline">&lt;- as.numeric(snp.data[,&quot;rs1117&quot;]) - 1</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>&#160; #&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ sex + rs1112 , family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ age + rs1112 , family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ sex + age + rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ rs1117 + rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;anova (result.adj, test=&quot;Chi&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ rs1112 + rs1117, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;anova (result.adj, test=&quot;Chi&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = lm (trait ~ rs1112, data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = lm (trait ~ sex + rs1112, data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.inter = glm (affection ~ sex * rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.inter)&lt;br data-attributes=&quot;%20/&quot; /&gt;result.inter = glm (affection ~ age * rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.inter)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.inter = glm (affection ~ rs1112 * rs1117, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.inter)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;q()</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>&#160; #&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ sex + rs1112 , family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ age + rs1112 , family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ sex + age + rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ rs1117 + rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;anova (result.adj, test=&quot;Chi&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ rs1112 + rs1117, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;anova (result.adj, test=&quot;Chi&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = lm (trait ~ rs1112, data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = lm (trait ~ sex + rs1112, data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.inter = glm (affection ~ sex * rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.inter)&lt;br data-attributes=&quot;%20/&quot; /&gt;result.inter = glm (affection ~ age * rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.inter)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.inter = glm (affection ~ rs1112 * rs1117, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.inter)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;q()</div></td></tr> </table>

Serveradmin http://statgen.us/index.php?title=Regression_Exercise&diff=265&oldid=prev 2017-02-23T18:51:50Z

<p>Created page with &quot;__NOTITLE__ ==Regression exercise== In R: load(&quot;dbp.R&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;ls()&lt;br data-attributes=&quot;%20/&quot; /&gt;dbp[1:5,]&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attribut...&quot;</p> <p><b>New page</b></p><div>__NOTITLE__<br /> ==Regression exercise==<br /> In R:<br /> <br /> load(&quot;dbp.R&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;ls()&lt;br data-attributes=&quot;%20/&quot; /&gt;dbp[1:5,]&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.snp12 = glm (affection ~ rs1112, family=binomial(&quot;logit&quot;), data=dbp)&lt;br data-attributes=&quot;%20/&quot; /&gt;print (result.snp12)&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( class (result.snp12) )&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( summary(result.snp12) )&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;dev.geno = anova (result.snp12, test=&quot;Chi&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;lrt.pvalue = pchisq(dev.geno[dim(dev.geno)[1],&quot;Deviance&quot;],&lt;br data-attributes=&quot;%20/&quot; /&gt; df=2, ncp=0, FALSE)&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( lrt.pvalue )&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( summary(result.snp12)$coefficients )&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.beta = summary(result.snp12)$coefficients[2:3,1]&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( snp.beta )&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( exp(snp.beta) )&lt;br data-attributes=&quot;%20/&quot; /&gt;ci = confint (result.snp12)&lt;br data-attributes=&quot;%20/&quot; /&gt;print (ci)&lt;br data-attributes=&quot;%20/&quot; /&gt;print ( exp(ci) )&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.data = dbp[,c(&quot;affection&quot;, &quot;rs1112&quot;)]&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.data[,&quot;rs1112&quot;]&lt;br /&gt;summary(snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.all = glm (affection ~ rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;dev.all = anova (result.all, test=&quot;Chi&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.all)&lt;br data-attributes=&quot;%20/&quot; /&gt;print(dev.all)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.data = dbp[,c(&quot;affection&quot;, &quot;trait&quot;,&quot;sex&quot;, &quot;age&quot;, &quot;rs1112&quot;, &quot;rs1117&quot;)]&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;snp.data[,&quot;rs1112&quot;]&lt;br /&gt;snp.data[,&quot;rs1117&quot;] <br /> #&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ sex + rs1112 , family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ age + rs1112 , family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ sex + age + rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ rs1117 + rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;anova (result.adj, test=&quot;Chi&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = glm (affection ~ rs1112 + rs1117, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;anova (result.adj, test=&quot;Chi&quot;)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = lm (trait ~ rs1112, data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;result.adj = lm (trait ~ sex + rs1112, data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.adj)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.inter = glm (affection ~ sex * rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.inter)&lt;br data-attributes=&quot;%20/&quot; /&gt;result.inter = glm (affection ~ age * rs1112, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.inter)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;result.inter = glm (affection ~ rs1112 * rs1117, family=binomial(&quot;logit&quot;),&lt;br data-attributes=&quot;%20/&quot; /&gt; data=snp.data)&lt;br data-attributes=&quot;%20/&quot; /&gt;summary(result.inter)&lt;br data-attributes=&quot;%20/&quot; /&gt;#&lt;br data-attributes=&quot;%20/&quot; /&gt;q()</div>

Serveradmin