README.md

In jmanitz/kangar00: Kernel Approaches for Nonlinear Genetic Association Regression

kangar00

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.

Citation

To cite the package kangar00 itself use:

• J. Manitz, S. Friedrichs, P. Burger, B. Hofner, N.T. Ha, S. Freytag, H. Bickeboeller (2017). kangar00: Kernel Approaches for Nonlinear Genetic Association Regression, R package version 1.0, https://CRAN.R-project.org/package=kangar00.

The size-adjusted kernel function is introduced in:

• S. Freytag, H. Bickeboeller, C.I. Amos, T. Kneib, M. Schlather (2012). A Novel Kernel for Correcting Size Bias in the Logistic Kernel Machine Test with an Application to Rheumatoid Arthritis. Human Heredity, 74, 97-108.

The network-based kernel function is introduced in:

• S. Freytag, J. Manitz, M. Schlather, T. Kneib, C.I. Amos, A. Risch, J. Chang-Claude, J. Heinrich, H. Bickeboeller (2013). A Network-Based Kernel Machine Test for the Identifcation of Risk Pathways in Genome-Wide Association Studies. Human Heredity, 76, 64-75.

The kernel boosting method is introduced in:

• S. Friedrichs, J. Manitz, P. Burger, C.I. Amos, A. Risch, J.C. Chang-Claude, H.E. Wichmann, T. Kneib, H. Bickeboeller, and B. Hofner (2017). Pathway-Based Kernel Boosting for the Analysis of Genome-Wide Association Studies. Computational and Mathematical Methods in Medicine, 2017(6742763), 1-17. doi:10.1155/2017/6742763.

Use toBibtex(citation("kangar00")) in R to extract BibTeX references.

jmanitz/kangar00 documentation built on Jan. 7, 2023, 11:26 a.m.