Sib-pair Command: wqls


ClassAnalysis and data manipulation command
Namewqls
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


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