Meta / Cochran-Mantel-Haenszel Analysis Example¶
This example demonstrates Cochran-Mantel-Haenzsel chi-squared, CMH chi-squared trend and meta odds ratio testing of 3 studies and one marker. If you have problems opening a file, at the error page try using toolbar View, Source or click on Page, View Source to view the file.
Files required to run this example are :
MetaPedigree1.dat - Linkage pre-makeped pedigree file with a header lineMetaPedigree2.dat - Linkage pre-makeped pedigree file with a header lineMetaPedigree3.dat - Linkage pre-makeped pedigree file with a header lineMeta.rgen - .rgen parameter file
Output file of this analysis is :
Meta.report - full detail reportMeta.summary - ASCII summary report
To run this analysis:
java -jar Genie.jar PedGenie Meta.rgen
MetaPedigree1.datThis example pedigree file is composed of nuclear families consisting of 200 affected sib-pairs plus parents, 200 discordant sib-pairs plus parents, and 200 independent controls.
MetaPedigree2.datThis example pedigree file is composed of four-generation families consisting of 53 members per pedigree (sibships of size three in all generations, all sibs marry in generations 2 and 3) and 500 independent controls.
MetaPedigree3.datThis example pedigree file is composed of 1,000 independent cases and 1,000 independent controls.
Meta.rgenThe set-up of Meta.rgen is similar to the set-up of the SingleLocus.rgen. The major differences between the two files are, there are 3 genotypedata files for this example and it uses meta / CMH statistical analysis. It also output both summary and full report.
Meta.report output file
This Meta.report file is similar to the SingleLocus.report output. The exception is when CMH statistical tests are requested in a meta analysis of multiple data files, the individual study’s contingency tables and their test results specified by the user appear first, following the CMH / meta analysis statistics.
Meta.summary output file
This space-delimited file is a summary of all statistics, confidence intervals for odds ratios, and p-values for each individual study and CMH / meta analysis that appear in the Meta.report file. This allows the user to import results into other programs, such as Microsoft Excel. Each row of the summary file corresponds to each requested analysis. Format: markers, model type, random seed, individual study statistics followed by their corresponding p-values and odds ratio confidence intervals, CMH / meta statistics and their corresponding p-values and meta odds ratio confidence intervals.