Single Locus GeneCountAlleles Example¶
The Single Locus GeneCountAlleles example is similar to the Single Locus Example, but the allele frequency estimation method GeneCounter from GeneCountAlleles program is used. 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 :
PhasedPedigree.dat - Linkage pre-makeped pedigree file with a header linePhasedPedigree.par - Linkage Loci data fileTrait.dat - Trait / Covariate data fileSingleGeneCount.rgen - .rgen Parameter File
Output file :
To run this analysis:
java -jar Genie.jar PedGenie SingleGeneCount.rgen
PhasedPedigree.datThe example pedigree file is composed of 16 three generation families. Each individual has information on two markers.
Trait.datThe quantitative test requires a quantitative trait file. It contains the trait and covariate information for each individual.
SingleGeneCount.rgenThe SingleGeneCount.rgen is exactly the same as the SingleLocus.rgen file except the simulation method top=”GeneCounterTopSim” replaces the top=”AlleleFreqTopSim” method. Please see notes on SingleLocus.rgen for other details.
PhasedPedigree.parThis file is equivalent to a linkage data file. PedGenie uses allele frequencies from this file to statistically infer the genotypes of founders in a pedigree. Other lines in this file are required but ignored. Please see Alun Thomas web site for more information about this file.
SingleGeneCount.report output file
We refer users to the SingleLocus.report output for detailed information regarding the SingleGeneCount.report output file. We point out that the observed statistics for the SingleLocus.report and the SingleGeneCount.report files are the same for every analysis, as would be expected. However, the empirical p values differ between the two analyses because different allele frequency estimation methods were used.