Output 


The output file is called 'CC-QLStest.out'. It has

   General information : number of individuals phenotyped, number 
   of independent families 

   For each marker, 
     - the number of cases and controls genotyped,
     - allele frequencies estimated by naive counting in the case sample, 
       the control sample and the whole case+control sample
     - allele frequencies and s.d. 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.
     - value of the corrected chi2 statistic and corresponding p-value using the 
       chi2 distribution
     - value of the quasi-likelihood score statistic and corresponding p-value 
        using the chi2 distribution. 
     - the sign of the quasi-score 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 a the significant CC-QLS result.
     - a warning message is printed when some allele counts are small, a situation where
       the chi2 distribution might not provide accurate p-values

An error file called 'CC-QLStest.err' may contain warnings 
     - when individuals from the marker data file are not phenotyped
     - 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