kangar00: lkmt.net.kernel.hsa04020 – R documentation

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lkmt.net.kernel.hsa04020

Example test result for the network-based kernel for pathway hsa04020.

Description

An object of class lkmt containing exemplary test results for an application of the logistic kernel machine test, derived from the example data.

Usage

data(lkmt.net.kernel.hsa04020)

Format

An object of class lkmt for the network-based kernel and the pathway hsa04020.

formular: gives a formular defining the nullmodel used in the logistic kernel machine test
kernel: includes the kernel object of the pathway to be evaluated
GWASdata: gives the GWASdata object including the study data considered in testing
statistic: gives the value of the test statistic
df: specifies the degrees of freedom
p.value: includes teh p-value resulting from the test

Source

simulated data and Ensembl extract

Examples

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')

kangar00

Kernel Approaches for Nonlinear Genetic Association Regression

v1.4

GPL-2

Authors

Juliane Manitz [aut], Stefanie Friedrichs [aut], Patricia Burger [aut], Benjamin Hofner [aut], Ngoc Thuy Ha [aut], Saskia Freytag [ctb], Heike Bickeboeller [ctb]

Initial release

2020-02-12