http://genome.sph.umich.edu/w/index.php?action=history&feed=atom&title=METAL_Glucose_Example_Script 2026-09-24T03:27:17Z Revision history for this page on the wiki MediaWiki 1.43.1 http://genome.sph.umich.edu/w/index.php?title=METAL_Glucose_Example_Script&diff=808&oldid=prev 2010-03-30T11:14:50Z

<p>Created page with &#039;&lt;source lang=&quot;text&quot;&gt; # This file includes a series of comments. Each comment is marked # by a # character as the first character in the line. # # This is a comment! # Meta-anal…&#039;</p> <p><b>New page</b></p><div>&lt;source lang=&quot;text&quot;&gt;<br /> # This file includes a series of comments. Each comment is marked <br /> # by a # character as the first character in the line.<br /> #<br /> # This is a comment!<br /> <br /> # Meta-analysis weighted by standard error does not work well<br /> # when different studies used very different transformations.<br /> # In this case, some attempt was made to use similar trait<br /> # transformation and you can request a standard error based<br /> # analysis by uncommenting the following line:<br /> # SCHEME STDERR<br /> <br /> # Usually, it is a good to apply genomic control to each<br /> # input file. However, in this example, all the markers being<br /> # examined reside in strongly associated loci and it probably <br /> # is not a good idea. To find out what happens if you turn<br /> # on genomic control, uncomment the following line.<br /> # GENOMICCONTROL ON<br /> <br /> # To help identify allele flips, it can be useful to track<br /> # allele frequencies in the meta-analysis. To enable this<br /> # capability, uncomment the following two lines.<br /> # AVERAGEFREQ ON<br /> # MINMAXFREQ ON<br /> <br /> # To restric meta-analysis to two previously reported SNPs<br /> # and summarize study specific results, uncomment the two<br /> # lines that follow.<br /> # ADDFILTER SNP IN (rs10830963,rs563694)<br /> # VERBOSE ON<br /> <br /> # Describe and process the DGI input files<br /> MARKER SNP<br /> WEIGHT N<br /> ALLELE EFFECT_ALLELE NON_EFFECT_ALLELE<br /> FREQ EFFECT_ALLELE_FREQ<br /> EFFECT BETA<br /> STDERR SE<br /> PVAL P_VAL<br /> <br /> PROCESS DGI_three_regions.txt<br /> <br /> # Describe and process the FUSION input files<br /> MARKER SNP<br /> ALLELE EFFECT_ALLELE NON_EFFECT_ALLELE<br /> FREQ FREQ_EFFECT<br /> WEIGHT N<br /> EFFECT BETA<br /> STDERR SE<br /> PVAL PVALUE<br /> <br /> PROCESS MAGIC_FUSION_Results.txt.gz<br /> <br /> # Describe and process the SardiNIA input files<br /> MARKER SNP<br /> DEFAULT 4106<br /> ALLELE AL1 AL2<br /> FREQ FREQ1<br /> EFFECT EFFECT<br /> STDERR SE<br /> PVAL PVALUE<br /> <br /> PROCESS magic_SARDINIA.tbl<br /> <br /> # Execute meta-analysis<br /> ANALYZE<br /> &lt;/source&gt;</div>

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