CreateKernel: Computes the regularized laplacian matrix from an adjacency...
In lancour/ignition: INTEGRATION OF GENETIC ASSOCIATIONS WITH NETWORK DIFFUSION

Description Usage Arguments Value Examples

This method takes an adjacency matrix, which can be created with CreateAdjMatrix, and computes the diffusion kernel matrix. If the dimensions of the adjacency matrix are large (at least 10,000 x 10,000), then this step can take an hour or more to run.

1	CreateKernel(adj.mat, lambda = 0.1, normalize = FALSE, autosave = FALSE)

`adj.mat`	Required. An adjacency matrix. Can be produced using `CreateAdjMatrix`
`lambda`	Optional. Defaults to standard of 0.1. Adjusts the amount of diffusion done. Not recommended to change unless there is specific rationale for doing so.
`normalize`	Optional. Defaults to false. If set to true, the normalized version of the laplacian is computed prior to kernel computation.
`autosave`	Optional. Since this function can take a while to compute, it may be preferable to have the kernel be saved immediately once it is computed. If autosave is set to TRUE, a copy of the kernel will be saved in the current working directory.

The regularized laplacian kernel matrix.

data(ignition.example.edges)
adj.matrix = CreateAdjMatrix(ignition.example.edges)
kernel = CreateKernel(adj.matrix)   #if not using autosave
kernel = CreateKernel(adj.matrix,autosave=TRUE)    #if using autosave