GWASdata                S4 class for an object representing a
                        Genome-wide Assocaition Study.
anno                    Example annotation file for three pathways.
calc_kernel             Calculate the kernel-matrix for a pathway
geno                    Example genotypes for 50 individuals.
get_anno,snp_info,pathway_info-method
                        Annotates SNPs via genes to pathways
get_network_matrix      Function to calculate the network 'matrix' for
                        a 'pathway' object
gwas                    Example 'GWASdata' object.
hsa04020                Example 'pathway' object for pathway hsa04020.
hsa04022_info           Example 'pathway_info' object for 'pathway'
                        hsa04022.
kangar00-package        kangar00 package
kernel-class            An S4 class representing a kernel matrix
                        calculated for a pathway
lkmt-class              An S4 class to represent the variance component
                        test.
lkmt.net.kernel.hsa04020
                        Example test result for the network-based
                        'kernel' for 'pathway' hsa04020.
lkmt_test               A function to calculate the p-values for kernel
                        matrices.
lowrank_kernel-class    An S4 class to represent a low-rank kernel for
                        a SNPset at specified knots
make_psd,matrix-method
                        Adjust network 'matrix' to be positive
                        semi-definite
net.kernel.hsa04020     Example network-based kernel matrix for pathway
                        hsa04020.
pathway                 An S4 class to represent a gene-gene
                        interaction network
pathway_info            An S4 class for an object assigning genes to
                        pathways
pheno                   Example phenotype file for 50 individuals.
read_geno,character-method
                        read genotype data from file to one of several
                        available objects, which can be passed to a
                        GWASdata object 'GWASdata'.
rewire_network          Rewires interactions in a 'pathway', which go
                        through a gene not represented by any SNPs in
                        the considered 'GWASdata' dataset.
rs10243170_info         Example 'snp_info' object for SNP rs10243170.
snp_info                An S4 class for an object assigning SNP
                        positions to rs-numbers (for internal use)
