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kangar00 (version 1.1)

Kernel Approaches for Nonlinear Genetic Association Regression

Description

Methods to extract information on pathways, genes and 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.

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Version

Install

install.packages('kangar00')

Monthly Downloads

662

Version

1.1

License

GPL-2

Maintainer

Juliane Manitz

Last Published

August 8th, 2017

Functions in kangar00 (1.1)

calc_kernel

Calculates the kernel-matrix for a pathway
gene_name_number,character-method

Function to get genes names and numbers from kegg (for internal use)
geno

Example genotypes for 50 individuals.
get_ana,data.frame-method

Produce middle part of network kernel (for internal use)
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.
GWASdata

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

Example annotation file for three pathways.
lowrank_kernel-class

An S4 class to represent a low-rank kernel for a SNPset at specified knots
make_psd,matrix-method

Adjust network matrix to be positive semi-definite
get_anno,snp_info,pathway_info-method

Annotates SNPs via genes to pathways
get_network_matrix,pathway-method

Function to calculate the network matrix for a pathway object
net.kernel.hsa04020

Example network-based kernel matrix for pathway hsa04020.
pathway

An S4 class to represent a gene-gene interaction network
read_geno,character-method

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

An S4 class representing a kernel matrix calculated for a pathway
lkmt-class

An S4 class to represent the variance component test.
pathway_info

An S4 class for an object assigning genes to pathways
gwas

Example GWASdata object.
hsa04020

Example pathway object for pathway hsa04020.
hsa04022_info

Example pathway_info object for pathway hsa04022.
pheno

Example phenotype file for 50 individuals.
rewire_network

Rewires interactions in a pathway, which go through a gene not represented by any SNPs in the considered GWASdata dataset.
kangar00-package

kangar00 package
set_one,matrix-method

Helper function to set matrix entries to 0/1/-1 only
snp_info

An S4 class for an object assigning SNP positions to rs-numbers (for internal use)
rs10243170_info

Example snp_info object for SNP rs10243170.
set_names,matrix-method

Helper function to translate gene numbers to names