R: Kernel Approaches for Nonlinear Genetic Association Regression

# Kernel Approaches for Nonlinear Genetic Association Regression

## Documentation for package ‘kangar00’ version 1.4.2

- DESCRIPTION file

## Help Pages

kangar00-package | kangar00 package
analyze | An S4 class to represent a gene-gene interaction network
analyze-method | An S4 class to represent a gene-gene interaction network
anno | Example annotation file for three pathways.
ANY-method | An S4 class to represent a gene-gene interaction network
calc_kernel | Calculate the kernel-matrix for a pathway
calc_kernel-method | Calculate the kernel-matrix for a pathway
character | read genotype data from file to one of several available objects, which can be passed to a GWASdata object 'GWASdata'.
davies_test-method | A function to calculate the p-values for kernel matrices.
GeneSNPsize | S4 class for an object representing a Genome-wide Assocaition Study.
GeneSNPsize-method | S4 class for an object representing a Genome-wide Assocaition Study.
geno | Example genotypes for 50 individuals.
get_anno | Annotates SNPs via genes to pathways
get_anno-method | Annotates SNPs via genes to pathways
get_genes | An S4 class to represent a gene-gene interaction network
get_genes-method | An S4 class to represent a gene-gene interaction network
get_network_matrix | Function to calculate the network 'matrix' for a 'pathway' object
get_network_matrix-method | Function to calculate the network 'matrix' for a 'pathway' object
gwas | Example 'GWASdata' object.
GWASdata | S4 class for an object representing a Genome-wide Assocaition Study.
GWASdata-method | S4 class for an object representing a Genome-wide Assocaition Study.
hsa04020 | Example 'pathway' object for pathway hsa04020.
hsa04022_info | Example 'pathway_info' object for 'pathway' hsa04022.
kangar00 | kangar00 package
kernel | An S4 class representing a kernel matrix calculated for a pathway
kernel-class | An S4 class representing a kernel matrix calculated for a pathway
lin_kernel | Calculate the kernel-matrix for a pathway
lin_kernel-method | Calculate the kernel-matrix for a pathway
lkmt | An S4 class to represent the variance component test.
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 | An S4 class to represent a low-rank kernel for a SNPset at specified knots
lowrank_kernel-class | An S4 class to represent a low-rank kernel for a SNPset at specified knots
make_psd | Adjust network 'matrix' to be positive semi-definite
make_psd-method | Adjust network 'matrix' to be positive semi-definite
matrix | Adjust network 'matrix' to be positive semi-definite
net.kernel.hsa04020 | Example network-based kernel matrix for pathway hsa04020.
net_kernel | Calculate the kernel-matrix for a pathway
net_kernel-method | Calculate the kernel-matrix for a pathway
pathway | An S4 class to represent a gene-gene interaction network
pathway-method | An S4 class to represent a gene-gene interaction network
pathway2igraph | An S4 class to represent a gene-gene interaction network
pathway2igraph-method | An S4 class to represent a gene-gene interaction network
pathway_info | An S4 class for an object assigning genes to pathways
pathway_info-method | An S4 class for an object assigning genes to pathways
pheno | Example phenotype file for 50 individuals.
plot-method | An S4 class representing a kernel matrix calculated for a pathway
plot-method | An S4 class to represent a gene-gene interaction network
read_geno | read genotype data from file to one of several available objects, which can be passed to a GWASdata object 'GWASdata'.
read_geno-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.
rewire_network-method | 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.
sample_genes | An S4 class to represent a gene-gene interaction network
sample_genes-method | An S4 class to represent a gene-gene interaction network
score_test-method | A function to calculate the p-values for kernel matrices.
show-method | S4 class for an object representing a Genome-wide Assocaition Study.
show-method | An S4 class representing a kernel matrix calculated for a pathway
show-method | An S4 class to represent the variance component test.
show-method | An S4 class to represent a gene-gene interaction network
show-method | An S4 class for an object assigning genes to pathways
show-method | An S4 class for an object assigning SNP positions to rs-numbers (for internal use)
sia_kernel | Calculate the kernel-matrix for a pathway
sia_kernel-method | Calculate the kernel-matrix for a pathway
snp_info | An S4 class for an object assigning SNP positions to rs-numbers (for internal use)
snp_info-method | An S4 class for an object assigning SNP positions to rs-numbers (for internal use)
summary-method | S4 class for an object representing a Genome-wide Assocaition Study.
summary-method | An S4 class representing a kernel matrix calculated for a pathway
summary-method | An S4 class to represent the variance component test.
summary-method | An S4 class to represent a gene-gene interaction network
summary-method | An S4 class for an object assigning genes to pathways
summary-method | An S4 class for an object assigning SNP positions to rs-numbers (for internal use)