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Three different kernel\nfunctions are offered to analyze genotype information in this\nvariance component test: A linear kernel, a size-adjusted\nkernel and a network-based kernel).", "License": "GPL-2", "Encoding": "UTF-8", "Collate": "'pathway.r' 'GWASdata.r' 'data.R' 'get_network_matrix.r'\n'kernel.r' 'lkmt.r'", "LazyData": "true", "NeedsCompilation": "no", "RoxygenNote": "7.3.1", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://jmanitz.r-universe.dev", "Date/Publication": "2024-09-09 16:43:42 UTC", "RemoteUrl": "https://github.com/jmanitz/kangar00", "RemoteRef": "HEAD", "RemoteSha": "a91c39f643e9f8c9d073478f3694efe42f65b357", "Packaged": { "Date": "2026-05-26 09:04:48 UTC", "User": "root" }, "Author": "Juliane Manitz [aut, cre],\nBenjamin Hofner [aut],\nStefanie Friedrichs [aut],\nPatricia Burger [aut],\nNgoc Thuy Ha [aut],\nSaskia Freytag [ctb],\nHeike Bickeboeller [ctb]", "Maintainer": "Juliane Manitz ", "MD5sum": "8ed4cda275ed7780458b31436fbf82e8", 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"rs8365742", "rs1672937", "rs7446869", "rs1234659", "rs2766237", "rs2942753", "rs3882459", "rs4228195", "rs9767895", "rs4833876", "rs1174932", "rs2784691", "rs9563496", "rs6496263", "rs5483437", "rs7667696", "rs9433427", "rs1885847", "rs7595917", "rs6669497", "rs4586681", "rs2247391", "rs2847499", "rs6841935", "rs7684495", "rs2754118", "rs1711529", "rs6187856", "rs6382624", "rs7485822", "rs1389621", "rs6466272", "rs6963491", "rs9713719", "rs2513563", "rs4812445", "rs1126814", "rs5515316", "rs7732458", "rs9221113", "rs1462576", "rs9465645", "rs4693228", "rs3993653", "rs8158786", "rs2392386", "rs7494252", "rs1458741", "rs1111758", "rs4926163", "rs1826682", "rs3589935", "rs2783391", "rs9137717", "rs1118693", "rs8962252", "rs2324785", "rs5563258", "rs6915165", "rs6631444", "rs9219676", "rs4243193", "rs5965992", "rs3223625", "rs2184536", "rs3831139", "rs2531873", "rs6777925", "rs4238663", "rs5284145", "rs3918138", "rs1585526", "rs5939349", "rs1438152", "rs1976153", "rs7837244", "rs5642643", "rs1977889", "rs4722199", "rs9353627", "rs7335772", "rs7839292", "rs3185922", "rs1883832", "rs1818439", "rs1373279", "rs5522859", "rs8451974", "rs4494382", "rs7995529", "rs9572866", "rs9172867", "rs5944114", "rs4866888", "rs5649646", "rs3824892", "rs1999715", "rs4234886", "rs4394832", "rs6141645", "rs6847264", "rs7596591", "rs6995736", "rs9397845", "rs8137928", "rs4763467", "rs3797231", "rs8361247", "rs7289216", "rs4969335", "rs3974456", "rs2386133", "rs8214217", "rs5598375", "rs8934459", "rs5561824", "rs1611656", "rs6455217", "rs5962419", "rs1953325", "rs9193678", "rs4866727", "rs8399523", "rs5274452", "rs2512738", "rs6479358", "rs6595823", "rs5425891", "rs6147797", "rs8328239", "rs6816975", "rs4871292", "rs4583873", "rs2294848", "rs8895729", "rs2961587", "rs1975734", "rs5117814", "rs8937461", "rs1787486", "rs5936644", "rs4388338", "rs5355575", "rs1968342", "rs2254988", "rs2341232", "rs1518485", "rs8733195", "rs5878799", "rs1539346", "rs7937851", "rs9495592", "rs9821288", "rs1194641", "rs3218314", "rs1175566", "rs7663344", "rs8346361", "rs1658336", "rs4152571", "rs8216285", "rs8491252", "rs3341354", "rs4153318", "rs7145183", "rs4968952", "rs2486118", "rs7292792", "rs5335677", "rs9577642", "rs4958779", "rs7376444", "rs3244821", "rs1586749", "rs5256896", "rs9899618", "rs4842612", "rs2771371", "rs8449578", "rs2649349", "rs2724863", "rs4424832", "rs5675647", "rs9146728", "rs5539422", "rs9858686", "rs5795642", "rs9141243", "rs6442965", "rs2999143", "rs8937769", "rs2779985", "rs6223238", "rs5142939", "rs4367895", "rs6766368", "rs9943617", "rs1122531", "rs3553476", "rs2591119", "rs9789442", "rs5417562", "rs4866727", "rs8586227", "rs4418849", "rs3727377", "rs8975592", "rs6189888", "rs7259556", "rs5685626", "rs6728967", "rs1684769", "rs8552452", "rs5917949", "rs1484959", "rs4681134", "rs8273742", "rs7887255", "rs8673536", "rs3921815", "rs4636168", "rs3828548", "rs6755684", "rs9234342", "rs6254447", "rs9229578", "rs9261717", "rs1872225", "rs1749148", "rs8413631", "rs2718453", "rs2993791", "rs1152447", "rs1559216", "rs1362933", "rs9818478", "rs3616524", "rs3431362", "rs3785474", "rs6649477", "rs1565126", "rs3493436", "rs4467872", "rs3748225", "rs2782731", "rs4987868", "rs2914826", "rs6197958", "rs8979615", "rs6667195", "rs8286593", "rs7374825", "rs7783639", "rs9829687", "rs6261847", "rs7422568", "rs5743626", "rs8361225", "rs6576485", "rs7935944", "rs1672144", "rs3353922", "rs7662289", "rs8692156", "rs5355517", "rs8487668", "rs9135241", "rs2199978", "rs4828163", "rs4352236", "rs3392551", "rs1312825", "rs4838988", "rs6555678", "rs6926945", "rs5645367", "rs5866453", "rs4825715", "rs1737212", "rs3185166", "rs8572265", "rs9427627", "rs9469856", "rs1324913", "rs3427727", "rs4944147", "rs8246836", "rs6234549", "rs9161988", "rs3543358", "rs4313359", "rs7116483", "rs4172275", "rs9441851", "rs3697762", "rs3694919", "rs4373286", "rs4946589", "rs3221382", "rs6924861", "rs3191165", "rs3552894", "rs1921439", "rs8614362", "rs4924198", "rs4297373", "rs5333367", "rs2766857", "rs2569333", "rs7398174", "rs9998212", "rs5846149", "rs9219835", "rs3168898", "rs8517531", "rs6156551", "rs4599765", "rs8421528", "rs9555994", "rs6632726", "rs9824423", "rs9182919", "rs4582551", "rs6653579", "rs7182573", "rs6812248", "rs6363856", "rs1955721", "rs3228888", "rs8113288", "rs6379514", "rs6373472", "rs7255556", "rs9498889", "rs7535989", "rs1538524", "rs9759861", "rs5389737", "rs6757293", "rs5917472", "rs8212789", "rs8332366", "rs1662981", "rs8531664", "rs7938368", "rs3964425", "rs9483684", "rs3741747", "rs1615777", "rs6662672", "rs5984322", "rs6238538", "rs2718643", "rs9125566", "rs8712485", "rs4214564", "rs3367799", "rs2752837", "rs9245679", "rs4415494", "rs3718131", "rs6974642", "rs2421353", "rs9627774", "rs5526351", "rs4918693", "rs1231997", "rs9596876", "rs1342743", "rs6925274", "rs9259688", "rs1145863", "rs8516549", "rs5738473", "rs9564813", "rs1431539", "rs7592697", "rs7982395", "rs4884886", "rs8532963", "rs8944912", "rs4296142", "rs2729811", "rs6962867", "rs9689524", "rs6497368", "rs1518773", "rs6811311", "rs5372523", "rs3749886", "rs3192429", "rs4272383", "rs7432522", "rs6566969", "rs7175788", "rs8327949", "rs6323728", "rs1456915", "rs7613932", "rs4242681", "rs5932534", "rs4875229", "rs8984531", "rs1889418", "rs7112859", "rs4746697", "rs2837943", "rs2124843", "rs7899271", "rs8759714", "rs1571592", "rs7694321", "rs4266817", "rs6597141", "rs9545941", "rs3466717", "rs6295695", "rs8512357", "rs2655772", "rs9892115", "rs7965654", "rs1367458", "rs7957382", "rs8361549", "rs9582262", "rs5452318", "rs2829714", "rs9586259", "rs3145245", "rs3863877", "rs2885565", "rs9468717", "rs9282859", "rs8936411", "rs2324719", "rs5734676", "rs9774579", "rs8229293", "rs2254825", "rs2663868", "rs8924554", "rs8969144", "rs2684743", "rs9459944", "rs8789725", "rs2227245", "rs9538578", "rs9945377", "rs1788899", "rs1344193", "rs5983671", "rs8952929", "rs1935189", "rs1463943", "rs6817857", "rs8787618", "rs8861414", "rs2796794", "rs8967255", "rs4467624", "rs5231833", "rs9956766", "rs2254524", "rs3278839", "rs3116441", "rs7319899", "rs8213536", "rs9447521", "rs2229624", "rs7941544", "rs6395993", "rs3446642" ], "rows": 50, "table": true, "tojson": true }, { "name": "gwas", "title": "Example 'GWASdata' object.", "object": "gwas", "class": [ "GWASdata" ], "fields": [], "table": false, "tojson": false }, { "name": "hsa04020", "title": "Example 'pathway' object for pathway hsa04020.", "object": "hsa04020", "class": [ "pathway" ], "fields": [], "table": false, "tojson": false }, { "name": "hsa04022_info", "title": "Example 'pathway_info' object for 'pathway' hsa04022.", "object": "hsa04022_info", "class": [ "pathway_info" ], "fields": [], "table": false, "tojson": false }, { "name": "lkmt.net.kernel.hsa04020", "title": "Example test result for the network-based 'kernel' for 'pathway' hsa04020.", "object": "lkmt.net.kernel.hsa04020", "class": [ "lkmt" ], "fields": [], "table": false, "tojson": false }, { "name": "net.kernel.hsa04020", "title": "Example network-based kernel matrix for pathway hsa04020.", "object": "net.kernel.hsa04020", "class": [ "kernel" ], "fields": [], "table": false, "tojson": false }, { "name": "pheno", "title": "Example phenotype file for 50 individuals.", "object": "pheno", "class": [ "data.frame" ], "fields": [ "pheno", "sex", "age" ], "rows": 50, "table": true, "tojson": true }, { "name": "rs10243170_info", "title": "Example 'snp_info' object for SNP rs10243170.", "object": "rs10243170_info", "class": [ "snp_info" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "kangar00-package", "title": "kangar00 package", "topics": [ "kangar00-package", "kangar00" ] }, { "page": "anno", "title": "Example annotation file for three pathways.", "topics": [ "anno" ] }, { "page": "calc_kernel", "title": "Calculate the kernel-matrix for a pathway", "topics": [ "calc_kernel", "calc_kernel,GWASdata-method", "lin_kernel", "lin_kernel,GWASdata-method", "net_kernel", "net_kernel,GWASdata-method", "sia_kernel", "sia_kernel,GWASdata-method" ] }, { "page": "geno", "title": "Example genotypes for 50 individuals.", "topics": [ "geno" ] }, { "page": "get_anno-snp_info-pathway_info-method", "title": "Annotates SNPs via genes to pathways", "topics": [ "get_anno", "get_anno,snp_info,pathway_info-method" ] }, { "page": "get_network_matrix", "title": "Function to calculate the network 'matrix' for a 'pathway' object", "topics": [ "get_network_matrix", "get_network_matrix,pathway-method" ] }, { "page": "gwas", "title": "Example 'GWASdata' object.", "topics": [ "gwas" ] }, { "page": "GWASdata-class", "title": "S4 class for an object representing a Genome-wide Assocaition Study.", "topics": [ "GeneSNPsize", "GeneSNPsize,GWASdata-method", "GWASdata", "GWASdata,ANY-method", "show,GWASdata-method", "summary,GWASdata-method" ] }, { "page": "hsa04020", "title": "Example 'pathway' object for pathway hsa04020.", "topics": [ "hsa04020" ] }, { "page": "hsa04022_info", "title": "Example 'pathway_info' object for 'pathway' hsa04022.", "topics": [ "hsa04022_info" ] }, { "page": "kernel-class", "title": "An S4 class representing a kernel matrix calculated for a pathway", "topics": [ "kernel", "kernel-class", "plot,kernel,ANY-method", "plot,kernel,missing-method", "show,kernel-method", "summary,kernel,ANY-method", "summary,kernel-method" ] }, { "page": "lkmt_test", "title": "A function to calculate the p-values for kernel matrices.", "topics": [ "davies_test,matrix-method", "lkmt_test", "score_test,matrix-method" ] }, { "page": "lkmt-class", "title": "An S4 class to represent the variance component test.", "topics": [ "lkmt", "lkmt-class", "show,GWASdata,ANY-method", "show,lkmt-method", "summary,GWASdata,ANY-method", "summary,lkmt-method" ] }, { "page": "lkmt.net.kernel.hsa04020", "title": "Example test result for the network-based 'kernel' for 'pathway' hsa04020.", "topics": [ "lkmt.net.kernel.hsa04020" ] }, { "page": "lowrank_kernel-class", "title": "An S4 class to represent a low-rank kernel for a SNPset at specified knots", "topics": [ "lowrank_kernel", "lowrank_kernel-class" ] }, { "page": "make_psd-matrix-method", "title": "Adjust network 'matrix' to be positive semi-definite", "topics": [ "make_psd", "make_psd,matrix-method", "matrix" ] }, { "page": "net.kernel.hsa04020", "title": "Example network-based kernel matrix for pathway hsa04020.", "topics": [ "net.kernel.hsa04020" ] }, { "page": "pathway-class", "title": "An S4 class to represent a gene-gene interaction network", "topics": [ "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" ] }, { "page": "pathway_info-class", "title": "An S4 class for an object assigning genes to pathways", "topics": [ "pathway_info", "pathway_info,character-method", "show,pathway_info,ANY-method", "show,pathway_info-method", "summary,pathway_info,ANY-method", "summary,pathway_info-method" ] }, { "page": "pheno", "title": "Example phenotype file for 50 individuals.", "topics": [ "pheno" ] }, { "page": "read_geno-character-method", "title": "read genotype data from file to one of several available objects, which can be passed to a GWASdata object 'GWASdata'.", "topics": [ "character", "read_geno", "read_geno,character-method" ] }, { "page": "rewire_network", "title": "Rewires interactions in a 'pathway', which go through a gene not represented by any SNPs in the considered 'GWASdata' dataset.", "topics": [ "rewire_network", "rewire_network,pathway-method" ] }, { "page": "rs10243170_info", "title": "Example 'snp_info' object for SNP rs10243170.", "topics": [ "rs10243170_info" ] }, { "page": "snp_info-class", "title": "An S4 class for an object assigning SNP positions to rs-numbers (for internal use)", "topics": [ "show,snp_info-method", "snp_info", "snp_info,character-method", "summary,snp_info-method" ] } ], "_readme": "https://github.com/jmanitz/kangar00/raw/HEAD/README.md", "_rundeps": [ "BH", "bigmemory", "bigmemory.sri", "bit", "bit64", "blob", "cachem", "chron", "cli", "CompQuadForm", "cpp11", "data.table", "DBI", "fastmap", "glue", "gsubfn", "igraph", "lattice", "lifecycle", "magrittr", "Matrix", "memoise", "pkgconfig", "proto", "Rcpp", "rlang", "RSQLite", "sqldf", "uuid", "vctrs" ], "_score": 4.216756879729666, "_indexed": true, "_nocasepkg": "kangar00", "_universes": [ "jmanitz" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.2", "date": "2026-05-26T09:07:29.000Z", "distro": "noble", "commit": "a91c39f643e9f8c9d073478f3694efe42f65b357", "fileid": "cd159314b2887fbbfe39b1eea91d049bf49cf843e81e74a3bfce78be903e6989", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jmanitz/actions/runs/26442788590" }, { "r": 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