| Class | Analysis and data manipulation command |
| Name | mqls |
| Arguments | <binary trait>|<quantitative
trait>
[>|>=|<|<=|==|^=
>lt;threshold>] [prevalence <prevalence>] [kin <kinship-file>] [ridge <ridge_constant>] [robust|hwe] [wqls] |
Calculates the MQLS [Thornton & McPeek 2007], WQLS and modified-chi-square [Bourgain et al 2003] quasi-likelihood score tests of allelic association where the trait is binary, or above or below the given threshold if the trait is quantitative. The MQLS test requires an estimate of the trait prevalence, which can be specified by appending a value to the command, or preset using the set prev command.
These tests use the kinship matrix to adjust for the resulting score for familial correlations in trait phenotype and marker genotype.
The kin option allows one to read in a kinship matrix from an external file, and the ridge option allows this matrix to be augmented, if for example it is NPD.
The format of the kinship file is a header
ped1 id1 ped2 id2 kin Smith John Jones Jenny 0.125 ...
Followed by one line per pair of relatives for whom a kinship is being supplied (unspecified pairs are set to zero, or one if a self-pair).
The robust variance option is the default, but the hwe version can be selected.
Example:
>> mqls adjChol > 144 0.4 -------------------------------------------------- MQLS association testing for trait "adjChol" -------------------------------------------------- NOTE: Proband defined as trait value > 144.0000 Trait model prevalence = 0.4000 Marker Typed Allels Chi-square Asy P -------------- ------ ------ ---------- ------ ldl 46 2 10.8 0.0010 MQLS **
See also:
| set prevalence | fix population binary trait prevalence |
| assoc | allelic/genotypic association with a trait |
| << (wqls) | Up to index | >> (tdt) |