lkmt.net.kernel.hsa04020 | R Documentation |
kernel
for
pathway
hsa04020.An object of class lkmt
containing exemplary test results for an
application of the logistic kernel machine test, derived from the example data.
data(lkmt.net.kernel.hsa04020)
An object of class lkmt
for the network-based
kernel
and the pathway
hsa04020.
gives a formular defining the nullmodel used in the logistic kernel machine test
includes the kernel
object of the
pathway
to be evaluated
gives the GWASdata
object including the study data
considered in testing
gives the value of the test statistic
specifies the degrees of freedom
includes teh p-value resulting from the test
simulated data and Ensembl extract
data(hsa04020)
data(gwas)
net_kernel <- calc_kernel(gwas, hsa04020, knots=NULL, type='net', calculation='cpu')
lkmt_test(pheno ~ sex + age, net_kernel, gwas, method='satt')
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