Package: kangar00 1.4.1
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 (Friedrichs et al., 2017, <doi:10.1155/2017/6742763>).
Authors:
kangar00_1.4.1.tar.gz
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kangar00.pdf |kangar00.html✨
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
- 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.
Last updated 2 years agofrom:1055f38042. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 23 2024 |
| R-4.5-win | OK | Aug 23 2024 |
| R-4.5-linux | OK | Aug 23 2024 |
| R-4.4-win | OK | Aug 23 2024 |
| R-4.4-mac | OK | Aug 23 2024 |
| R-4.3-win | OK | Aug 23 2024 |
| R-4.3-mac | OK | Aug 23 2024 |
Exports:analyzecalc_kernelGeneSNPsizeget_annoget_genesget_network_matrixGWASdatakernellin_kernellkmtlkmt_testlowrank_kernelmake_psdnet_kernelpathwaypathway_infopathway2igraphplotread_genorewire_networksample_genesshowsia_kernelsnp_infosummary
Dependencies:AnnotationDbiaskpassBHbigmemorybigmemory.sriBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64bitopsblobcachemchroncliCompQuadFormcpp11crayoncurldata.tableDBIdbplyrdigestdplyrfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDatagluegraphgsubfnhmshttrhttr2igraphIRangesjsonliteKEGGgraphKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogressprotopurrrR6rappdirsRcppRCurlRgraphvizrlangRSQLiteS4VectorssqldfstringistringrsystibbletidyrtidyselectUCSC.utilsutf8uuidvctrswithrXMLxml2XVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| kangar00 package | kangar00-package kangar00 |
| Example annotation file for three pathways. | anno |
| Calculate the kernel-matrix for a pathway | calc_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 pathways | get_anno get_anno,snp_info,pathway_info-method |
| Function to calculate the network 'matrix' for a 'pathway' object | get_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 pathway | kernel 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 knots | lowrank_kernel lowrank_kernel-class |
| Adjust network 'matrix' to be positive semi-definite | make_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 network | analyze 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 pathways | pathway_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 |
