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. 



A file called 'MQLStest.pvalues' lists the p-values for every SNP for MQLS, corrected chi-squared statistic, and WQLS.

  

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