anno | Example annotation file for three pathways. |
calc_kernel | Calculate the kernel-matrix for a pathway |
gene_name_number-character-method | Function to get genes names and numbers from kegg (for... |
geno | Example genotypes for 50 individuals. |
get_ana-data.frame-method | Produce middle part of network kernel (for internal use) |
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'... |
gwas | Example 'GWASdata' object. |
GWASdata-class | S4 class for an object representing a Genome-wide Assocaition... |
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... |
lkmt-class | An S4 class to represent the variance component test. |
lkmt.net.kernel.hsa04020 | Example test result for the network-based 'kernel' for... |
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... |
make_psd-matrix-method | Adjust network 'matrix' to be positive semi-definite |
net.kernel.hsa04020 | Example network-based kernel matrix for pathway hsa04020. |
pathway-class | An S4 class to represent a gene-gene interaction network |
pathway_info-class | 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... |
rewire_network | Rewires interactions in a 'pathway', which go through a gene... |
rs10243170_info | Example 'snp_info' object for SNP rs10243170. |
set_names-matrix-method | Helper function to translate gene numbers to names |
set_one-matrix-method | Helper function to set 'matrix' entries to 0/1/-1 only |
snp_info-class | An S4 class for an object assigning SNP positions to... |
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