hapConstructor2.0 ExampleΒΆ
The hapConstructor2.0 example allows a user to examine the construction of haplotype analyses of a two loci using unphased data. 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 :
Genotype10Data.dat - Linkage pre-makeped pedigree file with a header line. Note that this contains a dataset with two unlinked genes merged into one data file. The markers are all specified in the rgen file, and there is a 0.5 distance value between the last marker in the first gene and the first marker in the second gene. hapConstructor2.0.rgen - .rgen Parameter File
Output files :
- hapConstructor2.0_1-0.build
- hapConstructor2.0_2-0.build
- hapConstructor2.0_3-0.build
- hapConstructor2.0_4-0.build
- hapConstructor2.0_5-0.build
- hapConstructor2.0_6-0.build
- all_obs.final
To run this analysis:
java -jar hapConstructor2.0.jar hapConstructor hapConstructor2.0.rgen
Genotype10Data.datThe example Genotype Data file is composed of 250 cases and 250 controls. Each individual has genotype data on 10 markers, 5 from gene1 and 5 from gene2.
hapConstructor_1-0.build
This file contains the tests that passed the threshold specified in the .rgen file. In this instance, the threshold for the first step was 0.1. The only SNP to pass the threshold and be used to construct the two locus analyses was SNP 2. To interpret the output in the file, each line has the values from a particular test. The line has SNP#:Model:Statistical Test: Observed statistic: P-value (i.e. 2:Allele:Chi-squared:70.103704:5.0E-4 means the Chi-square statistic for the allelic model had a p-value of 5.0e-4 and an observed statistic of 70.103704). Note that the tests for SNP 2 reached the lowest possible p-value (5.0e-4) given 2,000 simulations used, which would stop the build process by default if the parameter hapc_check_mostsignificant was not set to false.
hapConstructor_2-0.build
This file is read the same as hapConstructor_1-0.build, but it contains the tests that passed the threshold for the second step (two locus analyses), which was set to 0.05.
hapConstructor_n-0.buildThis file contains the results which passed the threshold for step n.
all_obs.final
This file contains all the test conducted throughout the build process for the observed data. The lines are similar to the .build files, but the first value in the string contains the significance run. For the observed data, the significance run is always -1. If sigtesting parameter was set to true, a file called all_sims.final would be produced. The lines in the all_sims.final file contain all the tests conducted from each simulated dataset put through the build process, and the first value indicates which simulated dataset the test came from.
Additional example dataset involving 14 markers in gene 1 and 11 markers in gene 2 are available with the project. Genotype data file