kangar00 (version 1.1)

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

Details

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

Examples

# NOT RUN {
data(gwas)
calc_kernel(gwas, hsa04020, knots=gwas, type='lin', calculation='cpu') 
# }
# NOT RUN {
gwas2 <- new('GWASdata', pheno=pheno[1:10,], geno=geno[1:10,], anno=anno, desc=" study 2")
calc_kernel(gwas, hsa04020, knots = gwas2, type='net', calculation='cpu')
# }