kangar00 (version 1.4.1)

lowrank_kernel-class: An S4 class to represent a low-rank kernel for a SNPset at specified knots

Description

An S4 class to represent a low-rank kernel for a SNPset at specified knots

Slots

type

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

kernel

kernel matrix of dimension equal to individuals

pathway

pathway object

Author

Juliane Manitz

Details

This kernel is used for predictions. If observations and knots are equal, better construct a full-rank kernel of class kernel.

Examples

data(gwas)
data(hsa04020)
square <- calc_kernel(gwas, hsa04020, knots=gwas, type='lin', calculation='cpu')
dim(square@kernel)

gwas2 <- new('GWASdata', pheno=pheno[1:10,], geno=geno[1:10,], anno=anno, desc="study 2")
low_rank <- calc_kernel(gwas, hsa04020, knots = gwas2, type='net', calculation='cpu')
dim(low_rank@kernel)