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kangar00 (version 1.4)

Kernel Approaches for Nonlinear Genetic Association Regression

Description

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 (Friedrichs et al., 2017, ).

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Version

Install

install.packages('kangar00')

Monthly Downloads

662

Version

1.4

License

GPL-2

Maintainer

Juliane Manitz

Last Published

February 17th, 2020

Functions in kangar00 (1.4)

get_anno,snp_info,pathway_info-method

Annotates SNPs via genes to pathways
get_network_matrix

Function to calculate the network matrix for a pathway object
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
read_geno,character-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.
GWASdata

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

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

Example annotation file for three pathways.
lkmt.net.kernel.hsa04020

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

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

Produce middle part of network kernel (for internal use)
pheno

Example phenotype file for 50 individuals.
gwas

Example GWASdata object.
calc_kernel

Calculate the kernel-matrix for a pathway
pathway

An S4 class to represent a gene-gene interaction network
hsa04020

Example pathway object for pathway hsa04020.
net.kernel.hsa04020

Example network-based kernel matrix for pathway hsa04020.
set_one,matrix-method

Helper function to set matrix entries to 0/1/-1 only
kangar00-package

kangar00 package
rs10243170_info

Example snp_info object for SNP rs10243170.
snp_info

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

Function to get genes names and numbers from kegg (for internal use)
hsa04022_info

Example pathway_info object for pathway hsa04022.
set_names,matrix-method

Helper function to translate gene numbers to names