This package includes methods to extract information on pathways, genes and SNPs from online databases and to evaluate these data using the logistic kernel machine test (LKMT) (Liu et al. 2008).
We defined SNP sets representing genes and whole pathways using knowledge on gene membership and interaction from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (Kanehisa et al. 2014). SNPs are mapped to genes via base pair positions of SNPs and transcript start and end points of genes as documented in the Ensemble database (Cunningham et al. 2015).
In the LKMT, we employed the linear kernel (Wu et al. 2010) as well as two more advanced kernels, adjusting for size bias in the number of SNPs and genes in a pathway (size-adjusted kernels), and incorporating the network structure of genes within the pathway (pathway kernels), respectively (Freytag et al. 2012, 2014). P-values are derived in a variance component test using a moment matching method (Schaid, 2010) or Davies' algorithm (Davies, 1980).
Juliane Manitz [aut], Stefanie Friedrichs [aut], Patricia Burger [aut],
Benjamin Hofner [aut], Ngoc Thuy Ha [aut], Saskia Freytag [ctb],
Heike Bickeboeller [ctb]
Maintainer: Juliane Manitz <r@manitz.de>
| Package: | kangar00 |
| Version: | 1.1 |
| Date: | 2017-08-07 |
| License: | GPL-2 |
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