Package: kangar00 1.4.2

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).

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

kangar00_1.4.2.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
kangar00/json (API)

# Install 'kangar00' in R:
install.packages('kangar00', repos = c('https://jmanitz.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jmanitz/kangar00/issues

Pkgdown/docs site:https://kangar00.manitz.org

Datasets:
  • anno - Example annotation file for three pathways.
  • geno - Example genotypes for 50 individuals.
  • gwas - Example 'GWASdata' object.
  • hsa04020 - Example 'pathway' object for pathway hsa04020.
  • hsa04022_info - Example 'pathway_info' object for 'pathway' hsa04022.
  • lkmt.net.kernel.hsa04020 - Example test result for the network-based 'kernel' for 'pathway' hsa04020.
  • net.kernel.hsa04020 - Example network-based kernel matrix for pathway hsa04020.
  • pheno - Example phenotype file for 50 individuals.
  • rs10243170_info - Example 'snp_info' object for SNP rs10243170.

On CRAN:

Conda:

4.22 score 2 stars 21 scripts 3.9k downloads 1 mentions 25 exports 30 dependencies

Last updated from:a91c39f643. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK169
source / vignettesOK224
linux-release-x86_64OK164
macos-release-arm64OK158
macos-oldrel-arm64OK161
windows-develOK125
windows-releaseOK112
windows-oldrelOK115
wasm-releaseOK154

Exports:analyzecalc_kernelGeneSNPsizeget_annoget_genesget_network_matrixGWASdatakernellin_kernellkmtlkmt_testlowrank_kernelmake_psdnet_kernelpathwaypathway_infopathway2igraphplotread_genorewire_networksample_genesshowsia_kernelsnp_infosummary

Dependencies:BHbigmemorybigmemory.sribitbit64blobcachemchroncliCompQuadFormcpp11data.tableDBIfastmapgluegsubfnigraphlatticelifecyclemagrittrMatrixmemoisepkgconfigprotoRcpprlangRSQLitesqldfuuidvctrs

Readme and manuals

Help Manual

Help pageTopics
kangar00 packagekangar00-package kangar00
Example annotation file for three pathways.anno
Calculate the kernel-matrix for a pathwaycalc_kernel calc_kernel,GWASdata-method lin_kernel lin_kernel,GWASdata-method net_kernel net_kernel,GWASdata-method sia_kernel sia_kernel,GWASdata-method
Example genotypes for 50 individuals.geno
Annotates SNPs via genes to pathwaysget_anno get_anno,snp_info,pathway_info-method
Function to calculate the network 'matrix' for a 'pathway' objectget_network_matrix get_network_matrix,pathway-method
Example 'GWASdata' object.gwas
S4 class for an object representing a Genome-wide Assocaition Study.GeneSNPsize GeneSNPsize,GWASdata-method GWASdata GWASdata,ANY-method show,GWASdata-method summary,GWASdata-method
Example 'pathway' object for pathway hsa04020.hsa04020
Example 'pathway_info' object for 'pathway' hsa04022.hsa04022_info
An S4 class representing a kernel matrix calculated for a pathwaykernel kernel-class plot,kernel,ANY-method plot,kernel,missing-method show,kernel-method summary,kernel,ANY-method summary,kernel-method
A function to calculate the p-values for kernel matrices.davies_test,matrix-method lkmt_test score_test,matrix-method
An S4 class to represent the variance component test.lkmt lkmt-class show,GWASdata,ANY-method show,lkmt-method summary,GWASdata,ANY-method summary,lkmt-method
Example test result for the network-based 'kernel' for 'pathway' hsa04020.lkmt.net.kernel.hsa04020
An S4 class to represent a low-rank kernel for a SNPset at specified knotslowrank_kernel lowrank_kernel-class
Adjust network 'matrix' to be positive semi-definitemake_psd make_psd,matrix-method matrix
Example network-based kernel matrix for pathway hsa04020.net.kernel.hsa04020
An S4 class to represent a gene-gene interaction networkanalyze analyze,pathway-method ANY-method get_genes get_genes,pathway-method pathway pathway,ANY-method pathway2igraph pathway2igraph,pathway-method plot,pathway,ANY-method plot,pathway,missing-method sample_genes sample_genes,pathway-method show,pathway,ANY-method show,pathway-method summary,pathway,ANY-method summary,pathway-method
An S4 class for an object assigning genes to pathwayspathway_info pathway_info,character-method show,pathway_info,ANY-method show,pathway_info-method summary,pathway_info,ANY-method summary,pathway_info-method
Example phenotype file for 50 individuals.pheno
read genotype data from file to one of several available objects, which can be passed to a GWASdata object 'GWASdata'.character read_geno read_geno,character-method
Rewires interactions in a 'pathway', which go through a gene not represented by any SNPs in the considered 'GWASdata' dataset.rewire_network rewire_network,pathway-method
Example 'snp_info' object for SNP rs10243170.rs10243170_info
An S4 class for an object assigning SNP positions to rs-numbers (for internal use)show,snp_info-method snp_info snp_info,character-method summary,snp_info-method