Output 


The output file is called 'MQLStest.out'. It has

   General information : number of individuals, number of independent families 

   For each marker, 
     - among those genotyped at the marker, the numbers who are affected, 
       unaffected, and of unknown phenotype, respectively,
     - value of the MQLS statistic and corresponding p-value 
        using the chi-squared null distribution.
     - value of the corrected chi-squared statistic and corresponding p-value using the 
       chi-squared null distribution
     - value of the WQLS statistic and corresponding p-value 
        using the chi-squared null distribution. 
     - the signs of the MQLS and WQLS quasi-scores associated to each allele when the p-value is 
       smaller than 0.05, in order to know the direction of the change in allele
       frequency associated with the MQLS or WQLS result.
     - a warning message is printed when some allele counts are small, a situation in which
       the chi2 asymptotic null distribution might not provide accurate p-values
     - allele frequencies and s.d.'s estimated using the quasi-likelihood score function
       proposed by McPeek, Wu and Ober (2003) in the case sample, the control sample  
       and the case+control sample.
     - allele frequencies estimated by naive counting in the case sample, 
       the control sample and the whole case+control sample
   



A file called 'MQLStest.top' contains the top 20 markers with the smallest p-values.
The number of markers output to this file can be decreased or increased by the user by
changing MAXTOP (currently set to 20) in the MQLS.c source file. 


  


An error file called 'MQLStest.err' may contain warnings 
     - when lines have incorrect number of fields in the marker data file
     - when individuals from the kinship coefficient file are not listed 
       in the marker data file