An S4 class representing a kernel matrix calculated for a pathway
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
## 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, ...)
object |
An object of class |
x |
the |
y |
missing (placeholder). |
hclust |
|
... |
further arguments to be passed to the function. |
typeA character representing the kernel type: Use
'lin' for linear kernel, 'sia' for the size-adjusted
or 'net' for the network-based kernel.
kernelA kernel matrix of dimension equal to the number of individuals
pathwayA pathway object
Juliane Manitz
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)
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