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kangar00

Kernel Approaches for Nonlinear Genetic Association Regression

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, <doi:10.1155/2017/6742763>).

Functions (28)

GWASdata-class

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

anno

Example annotation file for three pathways.

calc_kernel

Calculate 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)

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

gwas

Example GWASdata object.

hsa04020

Example pathway object for pathway hsa04020.

hsa04022_info

Example pathway_info object for pathway hsa04022.

kangar00-package

kangar00 package

kernel-class

An S4 class representing a kernel matrix calculated for a pathway

lkmt-class

An S4 class to represent the variance component test.

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.

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

net.kernel.hsa04020

Example network-based kernel matrix for pathway hsa04020.

pathway-class

An S4 class to represent a gene-gene interaction network

pathway_info-class

An S4 class for an object assigning genes to pathways

pheno

Example phenotype file for 50 individuals.

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.

rs10243170_info

Example snp_info object for SNP rs10243170.

set_names-matrix-method

Helper function to translate gene numbers to names

set_one-matrix-method

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

snp_info-class

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

kangar00

Kernel Approaches for Nonlinear Genetic Association Regression

v1.4

GPL-2

Authors

Juliane Manitz [aut], Stefanie Friedrichs [aut], Patricia Burger [aut], Benjamin Hofner [aut], Ngoc Thuy Ha [aut], Saskia Freytag [ctb], Heike Bickeboeller [ctb]

Initial release

2020-02-12

kangar00

Functions (28)

kangar00

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