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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.
==ANALYZE HETEROGENEITY==
== ANALYZE HETEROGENEITY ==
'''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 || +
|-
|-
|}
|}
'''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 +
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
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
#meta-analysis can be performed at any stage
#and will include inputfiles 1-4
OUTFILE METAANALYSIS_inputfile1to4_ .tbl ANALYZE
#load the second half of inputfiles
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
# loading in the first half of inputfiles
#for the final meta-analysis of all 8 samples
#only output results if the combined weight
#is greater than 10000 people
# and will include inputfiles 1-4
OUTFILE METAANALYSIS_inputfile1-8_ .tbl MINWEIGHT 10000 ANALYZE
OUTFILE METAANALYSIS_inputfile1-8_ .tbl
MINWEIGHT 10000
ANALYZE
QUIT
QUIT EOT
EOT
