An S4 class to represent the variance component test.
show displays basic information on lkmt object
summary generates a lkmt object summary including the used kernel, pathway and the test result
# S4 method for lkmt
show(object)# S4 method for lkmt
summary(object)
show Basic information on lkmt object.
summary Summarized information on lkmt object.
An object of class lkmt.
formulaA formula stating the regression nullmodel that will be used in the variance component test.
kernelAn object of class kernel representing the similarity
matrix of the individuals based on which the pathways influence is evaluated.
GWASdataAn object of class GWASdata including the data
on which the test is conducted.
statisticA vector giving the value of the variance component
test statistic.
dfA vector containing the number of degrees of freedom.
p.valueA vector giving the p-value calculated for the pathway object considered in the variance component test.
For details on the variance component test see the references.
Juliane Manitz, Stefanie Friedrichs
Liu D, Lin X, Ghosh D: Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics 2007, 63(4):1079-88.
Wu MC, Kraft P, Epstein MP, Taylor DM, Chanock SJ, Hunter DJ, Lin X: Powerful SNP-Set Analysis for Case-Control Genome-Wide Association Studies. Am J Hum Genet 2010, 86:929-42
data(hsa04020)
data(gwas)
# compute kernel
net_kernel <- calc_kernel(gwas, hsa04020, knots=NULL, type='net', calculation='cpu')
# perform LKMT
res <- lkmt_test(pheno ~ sex + age, net_kernel, gwas, method='satt')
# show and summary methods
show(res)
summary(res)
# summary method
summary(lkmt.net.kernel.hsa04020)
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