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 |
| imports | bigmemory , biomaRt , CompQuadForm , data.table , igraph , KEGGgraph , lattice , methods , sqldf |
| depends | R (>= 3.1.0) |
| suggests | testthat |
| Contributors | Benjamin Hofner, Juliane Manitz, Saskia Freytag, Stefanie Friedrichs, Patricia Burger, Ngoc Ha, Heike Bickeboeller |
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