kernel-class: An S4 class representing a kernel matrix calculated for a...

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

An S4 class representing a kernel matrix calculated for a pathway

Description

An S4 class representing a kernel matrix calculated for a pathway

show displays the kernel object briefly

summary generates a kernel object summary including the number of individuals and genes for the pathway

plot creates an image plot of a kernel object

Usage

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

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

## S4 method for signature 'kernel,missing'
plot(x, y = NA, hclust = FALSE, ...)

Arguments

object	An object of class kernel
x	the kernel object to be plotted.
y	missing (placeholder).
hclust	logical, indicating whether a dendrogram should be added.
...	further arguments to be passed to the function.

Slots

type

A character representing the kernel type: Use 'lin' for linear kernel, 'sia' for the size-adjusted or 'net' for the network-based kernel.

kernel

A kernel matrix of dimension equal to the number of individuals

pathway

A pathway object

Author(s)

Juliane Manitz

Examples

data(gwas)
data(hsa04020)
net_kernel <- calc_kernel(gwas, hsa04020, knots=NULL, type='net', calculation='cpu')

show(net_kernel)
summary(net_kernel)
plot(net_kernel, hclust=TRUE)

jmanitz/kangar00 documentation built on Sept. 16, 2024, 2:14 a.m.