All functions


Example annotation file for three pathways.

calc_kernel(<GWASdata>) lin_kernel(<GWASdata>) sia_kernel(<GWASdata>) net_kernel(<GWASdata>)

Calculate the kernel-matrix for a pathway


Example genotypes for 50 individuals.


Annotates SNPs via genes to pathways


Function to calculate the network matrix for a pathway object


Example GWASdata object.

GWASdata() show(<GWASdata>) summary(<GWASdata>) GeneSNPsize(<GWASdata>)

S4 class for an object representing a Genome-wide Assocaition Study.


Example pathway object for pathway hsa04020.


Example pathway_info object for pathway hsa04022.

kangar00-package kangar00

kangar00 package

show(<kernel>) summary(<kernel>) plot(<kernel>,<missing>)

An S4 class representing a kernel matrix calculated for a pathway

show(<lkmt>) summary(<lkmt>)

An S4 class to represent the variance component test.

Example test result for the network-based kernel for pathway hsa04020.

lkmt_test() score_test(<matrix>) davies_test(<matrix>)

A function to calculate the p-values for kernel matrices.

lowrank_kernel-class lowrank_kernel

An S4 class to represent a low-rank kernel for a SNPset at specified knots


Adjust network matrix to be positive semi-definite


Example network-based kernel matrix for pathway hsa04020.

pathway() show(<pathway>) summary(<pathway>) pathway2igraph(<pathway>) analyze(<pathway>) get_genes(<pathway>) plot(<pathway>,<missing>) sample_genes(<pathway>)

An S4 class to represent a gene-gene interaction network

pathway_info() show(<pathway_info>) summary(<pathway_info>)

An S4 class for an object assigning genes to pathways


Example phenotype file for 50 individuals.


read genotype data from file to one of several available objects, which can be passed to a GWASdata object GWASdata.


Rewires interactions in a pathway, which go through a gene not represented by any SNPs in the considered GWASdata dataset.


Example snp_info object for SNP rs10243170.

snp_info() show(<snp_info>) summary(<snp_info>)

An S4 class for an object assigning SNP positions to rs-numbers (for internal use)