Difference between revisions of "SOCR EduMaterials AnalysesCommandLineFisherExact"

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This page includes the information on how to access the [http://socr.ucla.edu/htmls/SOCR_Analyses.html Fisher Exact Test] library via shell-based command-line interface on local machines. More information about [[SOCR_EduMaterials_AnalysesCommandLine | other SOCR Analyses command-line interfaces is available here]].
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This page includes the information on how to access the [http://en.wikipedia.org/wiki/Fisher%27s_exact_test Fisher Exact Test] library via shell-based command-line interface on local machines. More information about [[SOCR_EduMaterials_AnalysesCommandLine | other SOCR Analyses command-line interfaces is available here]].
  
 
== Introduction ==
 
== Introduction ==
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In addition to the graphical user interfaces, via a web-browser, all [http://socr.ucla.edu/htmls/SOCR_Analyses.html SOCR Analyses] allow command-line shell execution on local systems.
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In addition to the graphical user interfaces, via a web-browser, all [http://socr.umich.edu/html/ana/ SOCR Analyses] allow command-line shell execution on local systems.
  
 
==General Usage==
 
==General Usage==
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* Get the latest SOCR JAR files from the SOCR page (http://socr.ucla.edu/htmls/jars/).
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* Get the latest SOCR JAR files from the SOCR page (http://socr.umich.edu/html/jars/).
 
* The command-line interface to SOCR Analyses generally uses '''EXAMPLE 1''' from the list of example data files for the corresponding analysis.
 
* 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).
 
* All Input files are ASCII (see examples within each of the specific analyses).
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* a '''-h''' flag at the end of the command-line indicates that the first row in all ASCII input data files is a '''HEADER''' row (so it's not interpreted as data)
 
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* Number of variables have to be indicated at the end (after '''-h''' flag). If no number of variable is included, 5 is set defaulted.
 
  
 
==Fisher Exact Test Usage==
 
==Fisher Exact Test Usage==
 
* Generic Setting:
 
* Generic Setting:
 
<code>
 
<code>
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java -cp [SOCRjar_location]/SOCR_core.jar:[SOCRjar_location]/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.FisherExactCSV [data_location]/f.txt -h [number_of_variables] 5
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java -cp [SOCRjar_location]/SOCR_core.jar:[SOCRjar_location]/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.FisherExactCSV [data_location]/f.txt
 
</code>
 
</code>
  
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* Example: Edit a new file (FisherExactCSV.csh) using any editor and paste this inside (make sure the file has executable permisions). Some operating systems/platforms may require variants of this (C-shell) script.
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* 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.
 
<code>#!/bin/csh</code>
 
<code>#!/bin/csh</code>
  
 
<code>date</code>
 
<code>date</code>
  
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<code>java -cp /cxfs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_core.jar:/
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<code>java -cp /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_core.jar:/
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cxfs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_plugin.jar edu.ucla.
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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</code>
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stat.SOCR.analyses.command.FisherExactCSV /cxfs/ccb/CCB_SW_Tools/others/Statist
 
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ics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/f.txt -h 5</code>
 
  
 
<code>date</code>
 
<code>date</code>
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==Example Input data files==
 
==Example Input data files==
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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.
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One test datafile is included with the SOCR analyses command-line distribution ('''f.txt'''). The ASCII content of each of these is included below.
  
 
<center>
 
<center>
 
{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
 
{| class="wikitable" style="text-align:center" border="1" cellpadding="2"
 
|-
 
|-
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!  
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! colspan=5 | f.txt
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!
 
−
!
 
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! f.txt
 
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!
 
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|-
 
−
| A
 
−
| B
 
−
| C
 
−
| D
 
−
| E
 
 
|-
 
|-
 
| 5.0
 
| 5.0
 
| 4.0
 
| 4.0
−
| 7.0
 
−
| 10.0
 
−
| 12.0
 
 
|-
 
|-
 
| 1.0
 
| 1.0
 
| 3.0
 
| 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
 
 
|}
 
|}
 
</center>
 
</center>
  
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{{translate|pageName=http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFisherExact}}
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{{translate|pageName=http://wiki.socr.umich.edu/index.php?title=SOCR_EduMaterials_AnalysesCommandLineFisherExact}}

Latest revision as of 09:57, 5 March 2014

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.umich.edu/html/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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