lkmt-class | R Documentation |
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 signature 'lkmt' show(object) ## S4 method for signature 'lkmt' summary(object)
object |
An object of class |
show
Basic information on lkmt
object.
summary
Summarized information on lkmt
object.
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.
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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