lkmt-class function

An S4 class to represent the variance component test.

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 class

## S4 method for signature 'lkmt'
show(object)

## S4 method for signature 'lkmt'
summary(object)

Arguments

• object: An object of class lkmt.

Returns

show Basic information on lkmt object.

summary Summarized information on lkmt object.

Slots

• formula: A formula stating the regression nullmodel that will be used in the variance component test.

• kernel: An object of class kernel representing the similarity matrix of the individuals based on which the pathways influence is evaluated.

• GWASdata: An object of class GWASdata including the data on which the test is conducted.

• statistic: A vector giving the value of the variance component test statistic.

• df: A vector containing the number of degrees of freedom.

• p.value: A 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.
  

Examples

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)

References

• 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

Author(s)

Juliane Manitz, Stefanie Friedrichs