i-Gsea4Gwas Template Program beta Tutorial

Download i-GSEA4GWAS template program

i-GSEA4GWAS provides a JAVA template program to access web services directly. To run this program, JAVA environment is required. You can download the JVM software from http://java.sun.com/javase/downloads/index.jsp and set your proper system's environment to make sure the JAVA is executable.

Unzip the downloaded "i-Gsea4Gwas_v1.0.zip" file, which includes two jar files, "iGsea4Gwas.jar", "iGsea4Parse.jar" and one configuration file "iGSEA_Configuration.properties".

Gsea4Gwas.jar: this jar file is to run the main service of our server with the parameters in the file "iGSEA_Configuration.properties". Currently it only supports the SNP association data (-log(P-value), statistics or odds ratio) as input.

Command:

java -Xmx500m -jar iGsea4Gwas.jar configurationFile

The program will send the job to our server and the result file will be sent back to your computer, named "gene_set.txt".

You can modify the configuration file iGSEA_Configuration.properties as you like. For any questions about the parameters, please refers to the Tutorial of i-GSEA4GWAS or contact us by g4g@psych.ac.cn.

The main content of the configuration file (iGSEA_Configuration.properties) are as follows:

Job Name:                                   [test]                   /*  Set your job name.  */ 
Upload GWAS data file:                      [SNP_P_ValueManager.txt] /*  Modify it according to the name of your GWAS SNP association
                                                                         data file, and this parameter can NOT be blank  */
Select SNPs->genes mapping type:            [500kb]                  /*  Please select one of the three SNPs->genes mapping types: 
                                                                         500kb,100kb,5kb,within_gene,functional.  */
Gene set databases (canonical pathways):    [yes]                    /*  Put yes or no  */
Gene set databases (GO biological process): [no]                     /*  Put yes or no  */
Gene set databases (GO molecular function): [no]                     /*  Put yes or no  */
Gene set databases (GO cellular component): [no]                     /*  Put yes or no  */
Upload gene set file:                       []                       /*  Modify it according to the name of your gene set file, and leave 
                                                                         it as blank if you do not want to upload your own gene sets. */
Limit gene sets by keywords:                []                       /*  Can be any keywords including gene name  */
Keywords limitation:                        [include]                /*  Set the attribute include or exclude.   */
MHC/xMHC region mask:                       []                       /*  This property is limited to : blank or maskMHC or maskxMHC. */
Minimum number of genes in gene set:        [20]                     /*  The default minimum gene number is 20.  */
Maximum Number of genes in gene set:        [200]                    /*  The default maximum gene number is 200.  */ 

iGsea4Parse.jar: this jar file is to parse the result file obtained by iGsea4Gwas.jar.
Command:

java -Xmx500m -jar iGsea4Parse.jar -i gsea4gwasOutputFile -o parseOutputPath -q FDR _Value

gsea4gwasOutputFile is compulsory, it is the result file from iGsea4Gwas.jar, such as "gene_set.txt".

parseOutputPath is optional, current this directory is default if outputPath is null.

FDR_Value is optional in the range of [0, 0.25], and the default value is 0.05. This option is to set the cutoff for the gene sets to be extracted.

Parse result include two txt files and one folder named "ManhattanPlots":
1) gene_set_list.txt, which shows the significant gene set list the same content as the result page in web server.
2) gene_set_snp_info.txt, which shows the detailed information of each gene set.

All the Manhattan plots are generated in the folder "ManhattanPlots", and each Manhattan plot is named according to the corresponding gene set name.

In example folder, you can find some example files. SNP_P_ValueManager.txt is an example SNP association data file which is utilized for the demo run of i-GSEA4GWAS web server, iGSEA_Configuration.properties is a default configure file. In this folder, you can run

java -Xmx500m -jar iGsea4Gwas.jar

java -Xmx500m -jar iGsea4Parse.jar -i gene_set.txt