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.

f.txt
5.0	4.0
1.0	3.0

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