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 rxc.zip (http://www.niehs.nih.gov/research/atniehs/labs/bb/staff/zaykin/docs/rxc.zip) (328 KB)
For support: please contact Dmitri Zaykin (http://www.niehs.nih.gov/research/atniehs/labs/bb/staff/zaykin/index.cfm)
Installation
Start the "Command Prompt" window. (In Windows XP it is in Programs -> Accessories -> Command Prompt)
Change to the directory where you stored the programs, e.g. type "cd C:\MyStuff"
Run one of the programs to get help screen on its usage, e.g. type at the prompt "dz-rxc.exe" or "mcld.exe"
To run sample files downloaded from this directory, type "mcld.exe -file=loci.txt" or "dz-rxc.exe 10000 < rxcdat.txt"
you can direct output to a file as e.g. "dz-rxc.exe 10000 < rxcdat.txt > Results.txt"
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