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