
An S4 class to represent a low-rank kernel for a SNPset at specified knots
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
Juliane Manitz
This kernel is used for predictions. If observations and knots are
equal, better construct a full-rank kernel of class kernel
.
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)
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