Likelihood Ratio Test for Case-Control material. Software performs genotype-based and allele-based LRT tests and randomization test for calculating p-value.
Command is:
lrtcc case_file.txt control_file.txt number_of_replicates
Command line parameters are case file name, control file name and finally number of replicates. Number of replicates means how many times each marker genotypes will be randomized to determine empirical p-value.
Input files:
Case and Conrols file structures are identical.
line 1: number_markers_infile marker1_name marker2_name etc... line 2-: individual_id marker1_genotype marker2_genotype etc..
Example of case.dat and control.dat input files. Input files can have unlimited number of markers and individuals. Markers have to be in same order in case and control files.
Test statistics (genotype-based and allele-based LRT test) are printed to screen for each marker.
If one whish to redirect results to file, program can be run like this:
nohup nice lrtcc case.txt control.txt 10000 >& lrtcc.out &
And analysis are run on background and all output is redirected to lrtcc.out.
Tero Hiekkalinna and Joseph D. Terwilliger 2004.
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