kangar00 v1.4

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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 in kangar00

Name Description
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
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Details

Type Package
Date 2020-02-12
License GPL-2
Collate 'pathway.r' 'GWASdata.r' 'data.R' 'get_network_matrix.r' 'kernel.r' 'lkmt.r'
LazyData true
NeedsCompilation no
RoxygenNote 6.1.1
Packaged 2020-02-17 08:40:36 UTC; M254773
Repository CRAN
Date/Publication 2020-02-17 09:10:08 UTC

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