Man pages for jmanitz/kangar00
Kernel Approaches for Nonlinear Genetic Association Regression

annoExample annotation file for three pathways.
calc_kernelCalculate the kernel-matrix for a pathway
gene_name_number-character-methodFunction to get genes names and numbers from kegg (for...
genoExample genotypes for 50 individuals.
get_ana-data.frame-methodProduce middle part of network kernel (for internal use)
get_anno-snp_info-pathway_info-methodAnnotates SNPs via genes to pathways
get_network_matrixFunction to calculate the network 'matrix' for a 'pathway'...
gwasExample 'GWASdata' object.
GWASdata-classS4 class for an object representing a Genome-wide Assocaition...
hsa04020Example 'pathway' object for pathway hsa04020.
hsa04022_infoExample 'pathway_info' object for 'pathway' hsa04022.
kangar00-packagekangar00 package
kernel-classAn S4 class representing a kernel matrix calculated for a...
lkmt-classAn S4 class to represent the variance component test. test result for the network-based 'kernel' for...
lkmt_testA function to calculate the p-values for kernel matrices.
lowrank_kernel-classAn S4 class to represent a low-rank kernel for a SNPset at...
make_psd-matrix-methodAdjust network 'matrix' to be positive semi-definite
net.kernel.hsa04020Example network-based kernel matrix for pathway hsa04020.
pathway-classAn S4 class to represent a gene-gene interaction network
pathway_info-classAn S4 class for an object assigning genes to pathways
phenoExample phenotype file for 50 individuals.
read_geno-character-methodread genotype data from file to one of several available...
rewire_networkRewires interactions in a 'pathway', which go through a gene...
rs10243170_infoExample 'snp_info' object for SNP rs10243170.
set_names-matrix-methodHelper function to translate gene numbers to names
set_one-matrix-methodHelper function to set 'matrix' entries to 0/1/-1 only
snp_info-classAn S4 class for an object assigning SNP positions to...
jmanitz/kangar00 documentation built on Nov. 17, 2018, 2:14 p.m.