Description Usage Arguments Details Value Note Author(s) References See Also Examples
Under the assumption of HardyWeinberg equilibrium, a SNP genotype is
a binomial variate with two trials for an autosomal SNP or with one or
two trials (depending on sex) for a SNP on the X chromosome.
With each SNP in an input
"SnpMatrix"
as dependent variable, this function first fits a
"base" logistic regression model and then carries out a score test for
the addition of further term(s). The HardyWeinberg
assumption can be relaxed by use of a "robust" option.
1 2 3  snp.lhs.tests(snp.data, base.formula, add.formula, subset, snp.subset,
data = sys.parent(), robust = FALSE, uncertain = FALSE,
control=glm.test.control(), score=FALSE)

snp.data 
The SNP data, as an object of class

base.formula 
A 
add.formula 
A 
subset 
An array describing the subset of observations to be considered 
snp.subset 
An array describing the subset of SNPs to be considered. Default action is to test all SNPs. 
data 
The data frame in which 
robust 
If 
uncertain 
If 
control 
An object giving parameters for the IRLS algorithm
fitting of the base model and for the acceptable aliasing amongst
new terms to be tested. See 
score 
Is extended score information to be returned? 
The tests used are asymptotic chisquared tests based on the vector of
first and second derivatives of the loglikelihood with respect to the
parameters of the additional model. The "robust" form is a generalized
score test in the sense discussed by Boos(1992).
If a data
argument is supplied, the snp.data
and
data
objects are aligned by rowname. Otherwise all variables in
the model formulae are assumed to be stored in the same order as the
columns of the snp.data
object.
An object of class snp.tests.glm
or GlmTests.score
depending on whether score
is set to FALSE
or TRUE
in the call.
A factor (or
several factors) may be included as arguments to the function
strata(...)
in the base.formula
. This fits all
interactions of the factors so included, but leads to faster
computation than fitting these in the normal way. Additionally, a
cluster(...)
call may be included in the base model
formula. This identifies clusters of potentially correlated
observations (e.g. for members of the same family); in this case, an
appropriate robust estimate of the variance of the score test is used.
No more than one
strata()
call may be used, and neither strata(...)
or
cluster(...)
calls may appear in the add.formula
.
A known bug is that the function fails when no data
argument is
supplied and the base model formula contains no variables
(~1
). A workround is to create a data frame to hold the
variables in the models and pass this as data=
.
David Clayton [email protected]
Boos, Dennis D. (1992) On generalized score tests. The American Statistician, 46:327333.
GlmTestsclass
,
GlmTestsScoreclass
,
glm.test.control
,snp.rhs.tests
single.snp.tests
, SnpMatrixclass
,
XSnpMatrixclass
1 2 3 4  data(testdata)
snp.lhs.tests(Autosomes[,1:10], ~cc, ~region, data=subject.data)
snp.lhs.tests(Autosomes[,1:10], ~strata(region), ~cc,
data=subject.data)

Loading required package: survival
Loading required package: Matrix
Chi.squared Df p.value
173760 5.042958 9 0.8305475
173761 12.272003 9 0.1984058
173762 12.476151 9 0.1877771
173767 14.462676 9 0.1067926
173769 8.589652 9 0.4759812
173770 0.000000 0 1.0000000
173772 7.714914 9 0.5631116
173774 6.156140 9 0.7241952
173775 8.812111 9 0.4547958
173776 7.602749 9 0.5746207
Warning message:
In snp.lhs.tests(Autosomes[, 1:10], ~cc, ~region, data = subject.data) :
Monomorphic SNP: 6
Chi.squared Df p.value
173760 NaN 1 NaN
173761 1.4658701 1 0.2259984
173762 1.9149415 1 0.1664154
173767 0.7489825 1 0.3867986
173769 NaN 1 NaN
173770 NA NA NA
173772 NaN 1 NaN
173774 NaN 1 NaN
173775 NaN 1 NaN
173776 NaN 1 NaN
Warning message:
In snp.lhs.tests(Autosomes[, 1:10], ~strata(region), ~cc, data = subject.data) :
Monomorphic SNP: 6
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