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Correlation-Based Tests

Correlation-Based Tests for Phase Unknown Linkage Disequilibrium & Contingency Tables

The programs here are to accompany Zaykin, DV, Pudovkin AI, Weir BS 2008. Correlation-based inference for linkage disequilibrium with multiple alleles. Genetics (in press). They are compiled for Windows' "Command Line". The C++ source, developed under Linux (GNU compiler), is also provided.

 

  • dz-rxc.exe -- computes correlation-based tests for RxC contingency tables (as well as several other tests)
  • mcld.exe -- computes correlation-based tests for linkage disequilibrium. A sample input file is "loci.txt" in this directory (this file is modelled after LD found in STRs in Rosenberg NA et al., Science 2002; 298:2981-2985)

 

Downloads

  • Zipped file containing the C++ source, exe and txt documents: rxc.zip (396KB) Updated: 2010/01/13
  • For support: please contact Dmitri Zaykin("/Rhythmyx/assembler/render?sys_contentid=35225&sys_revision=5&sys_variantid=1278&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="1278" sys_dependentid="35225" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35225" sys_siteid="" sys_folderid="")

 

Installation

  1. Start the "Command Prompt" window. (In Windows XP it is in Programs -> Accessories -> Command Prompt)
  2. Change to the directory where you stored the programs, e.g. type "cd C:\MyStuff"
  3. Run one of the programs to get help screen on its usage, e.g. type at the prompt "dz-rxc.exe" or "mcld.exe"
  4. To run sample files downloaded from this directory, type "mcld.exe -file=loci.txt" or "dz-rxc.exe 10000 < rxcdat.txt"
  5. you can direct output to a file as e.g. "dz-rxc.exe 10000 < rxcdat.txt > Results.txt"

 

Contact

Dmitri Zaykin, Ph.D. (http://www.niehs.nih.gov/research/atniehs/labs/bb/staff/zaykin/index.cfm)
Principal Investigator
Tel (919) 541-0096
Fax (919) 541-4311
zaykind@niehs.nih.gov

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