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| METAL can also evaluate the evidence for heterogeneity. When you do this, METAL will do a second pass of analysis to decide whether observed effect sizes (or test statistics) are homogeneous across samples. This will result in a test statistic (with n-1) degrees of freedom for n samples. | | METAL can also evaluate the evidence for heterogeneity. When you do this, METAL will do a second pass of analysis to decide whether observed effect sizes (or test statistics) are homogeneous across samples. This will result in a test statistic (with n-1) degrees of freedom for n samples. |
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− | ==ANALYZE HETEROGENEITY== | + | == ANALYZE HETEROGENEITY == |
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− | '''Example 1; Strand flips required''' | + | '''Example 1; Strand flips required''' |
− | {| | + | |
| + | {| border="1" |
| |- | | |- |
− | ! | + | ! |
− | !ALLELES | + | ! ALLELES |
− | !EFFECT | + | ! EFFECT |
− | !ALLELES Analyzed | + | ! ALLELES Analyzed |
− | !EFFECT Analyzed | + | ! EFFECT Analyzed |
| |- | | |- |
− | |Input file 1, T/G, +, a/c, + | + | | Input file 1 || T/G || + || a/c || + |
− | |Input file 2, T/G, +, a/c, + | + | |- |
− | |Input file 3, A/C, +, a/c, + | + | | Input file 2 || T/G || + || a/c || + |
− | |Output, , , a/c, + | + | |- |
| + | | Input file 3 || A/C || + || a/c || + |
| + | | Output || || || a/c || + |
| |- | | |- |
| |} | | |} |
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− | '''Example 2; Reference allele flips required''' | + | '''Example 2; Reference allele flips required''' ALLELES EFFECT ALLELES Analyzed EFFECT Analyzed Input file 1 C/A - a/c + Input file 2 C/A - a/c + Input file 3 A/C + a/c + Output a/c + |
− | ALLELES EFFECT ALLELES Analyzed EFFECT Analyzed
| + | |
− | Input file 1 C/A - a/c + | + | Example 2; Strand flips, numeric flips, and reference allele flips required ALLELES EFFECT ALLELES Analyzed EFFECT Analyzed Input file 1 G/T - a/c + Input file 2 2/1 - a/c + Input file 3 A/C + a/c + Output a/c + |
− | Input file 2 C/A - a/c + | + | |
− | Input file 3 A/C + a/c + | + | <br> Example text file to run metal; |
− | Output a/c + | + | |
| + | #THIS FILE EXECUTES AN ANALYSIS OF ALL AVAILABLE INFORMATION |
| + | |
| + | mkdir output-metal |
| + | |
| + | metal << EOT |
| + | |
| + | #loading in the first half of inputfiles |
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− | Example 2; Strand flips, numeric flips, and reference allele flips required
| + | MARKER SNP ALLELE REF_ALLELE OTHER_ALLELE EFFECT BETA WEIGHT N PVALUE PVALUE PROCESS inputfile1.txt PROCESS inputfiles2.txt PVALUE pvalue ALLELE A_REF OTHER_ALLELE MARKER SNP EFFECT BETA WEIGHT N PROCESS inputfile3.txt MARKER MARKERNAME ALLELE EFFECTALLELE NON_EFFECT_ALLELE EFFECT EFFECT1 WEIGHT NONMISS PVALUE PVALUE PROCESS inputfile4.txt |
− | ALLELES EFFECT ALLELES Analyzed EFFECT Analyzed
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− | Input file 1 G/T - a/c +
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− | Input file 2 2/1 - a/c +
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− | Input file 3 A/C + a/c +
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− | Output a/c +
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− |
| + | #meta-analysis can be performed at any stage |
− | Example text file to run metal;
| + | #and will include inputfiles 1-4 |
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− | # THIS FILE EXECUTES AN ANALYSIS OF ALL AVAILABLE INFORMATION
| + | OUTFILE METAANALYSIS_inputfile1to4_ .tbl ANALYZE |
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− | mkdir output-metal
| + | #load the second half of inputfiles |
| | | |
− | metal << EOT
| + | MARKER rsid ALLELE EFFECT_ALLELE OTHER_ALLELE EFFECT BETA WEIGHT total_N PVALUE Add_p SEPARATOR COMMAS PROCESS inputfile5.txt PROCESS inputfile6.txt ALLELE ALLELE OTHER_ALLELE MARKER SNP EFFECT BETA WEIGHT N PVALUE PVALUE SEPARATOR WHITESPACE PROCESS inputfile7.txt ALLELE BETA_ALLELE OTHER_ALLELE PVALUE P_VAL MARKER SNP EFFECT BETA WEIGHT N PROCESS inputfile8.txt |
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− | # loading in the first half of inputfiles | + | #for the final meta-analysis of all 8 samples |
− | MARKER SNP
| + | #only output results if the combined weight |
− | ALLELE REF_ALLELE OTHER_ALLELE
| + | #is greater than 10000 people |
− | EFFECT BETA
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− | WEIGHT N
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− | PVALUE PVALUE
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− | PROCESS inputfile1.txt
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− | PROCESS inputfiles2.txt
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− | PVALUE pvalue
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− | ALLELE A_REF OTHER_ALLELE
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− | MARKER SNP
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− | EFFECT BETA
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− | WEIGHT N
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− | PROCESS inputfile3.txt
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− | MARKER MARKERNAME
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− | ALLELE EFFECTALLELE NON_EFFECT_ALLELE
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− | EFFECT EFFECT1
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− | WEIGHT NONMISS
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− | PVALUE PVALUE
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− | PROCESS inputfile4.txt
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− | # meta-analysis can be performed at any stage
| |
− | # and will include inputfiles 1-4 | |
− | OUTFILE METAANALYSIS_inputfile1to4_ .tbl
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− | ANALYZE
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| | | |
− | # load the second half of inputfiles
| + | OUTFILE METAANALYSIS_inputfile1-8_ .tbl MINWEIGHT 10000 ANALYZE |
− | MARKER rsid
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− | ALLELE EFFECT_ALLELE OTHER_ALLELE
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− | EFFECT BETA
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− | WEIGHT total_N
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− | PVALUE Add_p
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− | SEPARATOR COMMAS
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− | PROCESS inputfile5.txt
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− | PROCESS inputfile6.txt
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− | ALLELE ALLELE OTHER_ALLELE
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− | MARKER SNP
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− | EFFECT BETA
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− | WEIGHT N
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− | PVALUE PVALUE
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− | SEPARATOR WHITESPACE
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− | PROCESS inputfile7.txt
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− | ALLELE BETA_ALLELE OTHER_ALLELE
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− | PVALUE P_VAL
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− | MARKER SNP
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− | EFFECT BETA
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− | WEIGHT N
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− | PROCESS inputfile8.txt
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− | # for the final meta-analysis of all 8 samples
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− | # only output results if the combined weight
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− | # is greater than 10000 people
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− | OUTFILE METAANALYSIS_inputfile1-8_ .tbl | |
− | MINWEIGHT 10000 | |
− | ANALYZE | |
| | | |
− | QUIT | + | QUIT EOT |
− | EOT | |