Path2 Tutorial


If you have not already done so, download and unpack the Path2 software. Please see the Download page for instructions on how to install Path2.

The tutorial uses sample files which have been included in the Path2 package:

Path2/data/sampleData/asthma_pathway_rand_onlytrios.ped

Path2/data/sampleData/asthma_pathway.map

Path2/data/sampleData/gabriel_asthma_rs-P_fix.txt

gabriel_asthma_rs-P_fix.txt contains mappings of SNP to fixed effect model P-value as taken from the results file for the “GABRIEL Large-Scale Genome-Wide Association Study of Asthma”. It can be imported as an association results file in the Import data → Summary results tab. The data is publically available at the GABRIEL website. The file was generated using:
awk '{if (NR==1) {print "SNP\tP";} else {print $2,"\t",$11}}' gabriel_asthma_meta-analysis_36studies_format_repository_NEJM.txt >gabriel_asthma_rs-P_fix.txt .

asthma_pathway.ped and asthma_pathway.map contain genotype information on the KEGG asthma pathway genes. Genotypes were obtained from the HapMap CEU Phase 3 dataset. Phenotypes were randomly generated using the sampleData/randPhenotype.pl Perl script. See here for more information on how the sample data files were generated.

** PLEASE NOTE! Several of the Pathway tests (for example SNP Ratio Test) can take a very long time to run depending upon the size of the dataset. Genome-wide association study level datasets must be run on a dedicated computational cluster. At this time, it is highly recommended to first run Path2 on the sample synthetic asthma dataset provided with the application in “Path2/data/sampleData” to ensure your install is set up correctly, and to familiarize yourself with the application first. Moreover, a few potential problems with running Path2 on GWAS datasets have been identified and will addressed in future versions of the application. **

If you have any problems running the software, please check the FAQ before contacting us.


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