| Class | Analysis and data manipulation command |
| Name | wqls |
| Arguments | <trait>
[kin <kinship-file>] [ridge <ridge_constant>>] |
Calculates the WQLS [Bourgain et al 2003] quasi-likelihood score tests of allelic association where the trait is binary, categorical or quantitative.
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 (see mqls for more detail).
Example:
# # lmekin gives us: # Wald test = 22.54579 df = 1 p = 2.051937e-06 # LRTS = 16.23542 # merlin --fastassoc # Score = 12.59514 # merlin --assoc # - LINKAGE TEST RESULTS - ----- ASSOCIATION TEST RESULTS ---------- # H2 LOD pvalue Marker Allele Effect H2 LOD pvalue # 69.1% 3.92 1.1e-05 ldl 1 -0.372 15.41% 0.71 0.070 # mendel # LRTS = 21.20 # >> wqls adjChol -------------------------------------------------- WQLS association testing for trait "adjChol" -------------------------------------------------- Marker Typed Allels Chi-square Asy P -------------- ------ ------ ---------- ------ ldl 46 2 26.8 2e-7 WQLS *** >> mgt adjChol ------------------------------------------------ Measured genotype analysis for trait "adjChol" ------------------------------------------------ Marker Typed Allels Chi-square Asy P -------------- ------ ------ ---------- ------ ldl 46 2 16.2 6e-5
See also:
| mqls | MQLS allelic association |
| assoc | allelic/genotypic association with a trait |
| << (mgt) | Up to index | >> (mqls) |