public class GWAS_IFLPlugin
extends AbstractPlugin
The tables populated from this plugin are described in TAS-1162 The plugin takes files of gwas data and adds them to the gwas_data in a GOBII instance. It is assume the gwas_method and gwas_experiment tables associated with this data have already been populated. These are all proprietary tables currently only in use by Buckler Lab. TO speed up procesing, the experimentId and methodIds are hard-coded in the juint that calls this plugin. Those tables are generally small, and if you have to go to it to get the name, you might as well just input the ID anda save GOBII IFL processing time. The values stored in the "values" column will be stored as "real" in the gwas_data table This is because there is 1 "value" field, which holds values for all data, of any type. The method table will provide specifics on how to interpret each statistic. In addition to the .gz files of gwas data, a mapping file of phenotype names to IDs is created - data pulled from b4R table.
public GWAS_IFLPlugin(java.awt.Frame parentFrame,
boolean isInteractive)
public GWAS_IFLPlugin()
public javax.swing.ImageIcon getIcon()
public java.lang.String getButtonName()
public java.lang.String getToolTipText()
public static void main(java.lang.String[] args)
public java.lang.String inputFile()
Tab-delimited Input File containing a header line and entries, or Directory containing Tab-delimited files of gwas data. If parameter is a directory, each file must contain a header line, and the files must end with .txt or .txt.gz
public GWAS_IFLPlugin inputFile(java.lang.String value)
Set Input File. Tab-delimited Input File containing a header line and entries, or Directory containing Tab-delimited files of gwas data. If parameter is a directory, each file must contain a header line, and the files must end with .txt or .txt.gz
value - Input Filepublic java.lang.String methodIds()
Name of GWAS method as it appears in the name field of the gwas_method table
public GWAS_IFLPlugin methodIds(java.lang.String value)
Set Method Name. Name of GWAS method as it appears in the name field of the gwas_method table
value - Method Namepublic java.lang.String expID()
Name of the GWAS experiment to which this data belongs. This name must already exist in the name field of the gwas_experiment table.
public GWAS_IFLPlugin expID(java.lang.String value)
Set GWAS Experiment Name. Name of the GWAS experiment to which this data belongs. This name must already exist in the name field of the gwas_experiment table.
value - GWAS Experiment Namepublic java.lang.String statNames()
Comma separated list of column names from which to pull data. These names must match values in the statistics field of the gwas_method table for the specified method name.
public GWAS_IFLPlugin statNames(java.lang.String value)
Set Statistic Names. Comma separated list of column names from which to pull data. These names must match values in the statistics field of the gwas_method table for the specified method name.
value - Statistic Namespublic java.lang.String outputDir()
Full path name of directory to which output files will be written, must end with a /
public GWAS_IFLPlugin outputDir(java.lang.String value)
Set Path of output directory. Full path name of directory to which output files will be written, must end with a /
value - Path of output directorypublic java.lang.String b4rConfigFile()
DB config file containing connection information to the B4r database
public GWAS_IFLPlugin b4rConfigFile(java.lang.String value)
Set B4R Config File. DB config file containing connection information to the B4r database
value - B4R Config File