Kernel Approaches for Nonlinear Genetic Association Regression
Calculate the kernel-matrix for a pathway
Function to get genes names and numbers from kegg (for internal use)
Produce middle part of network kernel (for internal use)
Annotates SNPs via genes to pathways
Function to calculate the network matrix for a pathway object
S4 class for an object representing a Genome-wide Assocaition Study.
kangar00 package
An S4 class representing a kernel matrix calculated for a pathway
An S4 class to represent the variance component test.
A function to calculate the p-values for kernel matrices.
An S4 class to represent a low-rank kernel for a SNPset at specified k...
Adjust network matrix to be positive semi-definite
An S4 class to represent a gene-gene interaction network
An S4 class for an object assigning genes to pathways
read genotype data from file to one of several available objects, whic...
Rewires interactions in a pathway, which go through a gene not repre...
Helper function to translate gene numbers to names
Helper function to set matrix entries to 0/1/-1 only
An S4 class for an object assigning SNP positions to rs-numbers (for i...
Methods to extract information on pathways, genes and various single-nucleotid polymorphisms (SNPs) from online databases. It provides functions for data preparation and evaluation of genetic influence on a binary outcome using the logistic kernel machine test (LKMT). Three different kernel functions are offered to analyze genotype information in this variance component test: A linear kernel, a size-adjusted kernel and a network-based kernel).