net.kernel.hsa04020: Example network-based kernel matrix for pathway hsa04020.

In jmanitz/kangar00: Kernel Approaches for Nonlinear Genetic Association Regression

Example network-based kernel matrix for pathway hsa04020.

Description

An example of a kernel object.

Usage

data(net.kernel.hsa04020)

Format

An object of class kernel and type 'network' for the pathway hsa04020.

type

specifies which kernel function was used to calculate the kernel

kernel

includes the kernel matrix calculated for the pathway

pathway

includes the pathway object of the pathway, for which the kernel matrix was calculated

Source

simulated data and Ensembl extract

Examples

data(net.kernel.hsa04020)
# derivation 
data(gwas)
data(hsa04020)
net_kernel <- calc_kernel(gwas, hsa04020, knots=NULL, type='net', calculation='cpu')
# are the value differences smaller than machine epsilon?
all(abs(net.kernel.hsa04020@kernel - net_kernel@kernel) < sqrt(.Machine$double.eps))

jmanitz/kangar00 documentation built on Jan. 7, 2023, 11:26 a.m.