SOCR EduMaterials AnalysesCommandLineFisherExact
This page includes the information on how to access the Fisher Exact Test library via shell-based command-line interface on local machines. More information about other SOCR Analyses command-line interfaces is available here.
Introduction
In addition to the graphical user interfaces, via a web-browser, all SOCR Analyses allow command-line shell execution on local systems.
General Usage
- Get the latest SOCR JAR files from the SOCR page (http://socr.ucla.edu/htmls/jars/).
- The command-line interface to SOCR Analyses generally uses EXAMPLE 1 from the list of example data files for the corresponding analysis.
- All Input files are ASCII (see examples within each of the specific analyses).
Fisher Exact Test Usage
- Generic Setting:
java -cp [SOCRjar_location]/SOCR_core.jar:[SOCRjar_location]/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.FisherExactCSV [data_location]/f.txt
- Example: Edit a new file (FisherExactCSV.csh) using any editor and paste this inside (make sure the file has executable permissions). Some operating systems/platforms may require variants of this (C-shell) script.
#!/bin/csh
date
java -cp /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_core.jar:/
ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.FisherExactCSV /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/f.txt
date
exit
Example Input data files
One test datafile is included with the SOCR analyses command-line distribution (f.txt). The ASCII content of each of these is included below. Note that the first lines in these files are column headers. This requires the "-h" flag at the end of the command line execution so that these first lines are interpreted as column headers.
| f.txt | ||||
|---|---|---|---|---|
| A | B | C | D | E |
| 5.0 | 4.0 | 7.0 | 10.0 | 12.0 |
| 1.0 | 3.0 | 1.0 | 0.0 | 2.0 |
| 16.0 | 12.0 | 22.0 | 22.0 | 35.0 |
| 5.0 | 4.0 | 3.0 | 5.0 | 4.0 |
| 10.0 | 9.0 | 7.0 | 13.0 | 10.0 |
| 19.0 | 18.0 | 18.0 | 37.0 | 58.0 |
| 10.0 | 7.0 | 6.0 | 8.0 | 7.0 |
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