{ "_id": "6a1ef2d2b401979e73414afc", "Package": "KinformR", "Title": "Relationship-Informed Pedigree and Variant Scoring", "Version": "0.1.2", "Authors@R": "person(\"Cameron M.\", \"Nugent\", , \"cam.nugent@sequencebio.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-1135-2605\"))", "Maintainer": "Cameron M. Nugent ", "Description": "Comparative evaluation of families and candidate variants\nin rare-variant association studies. The package can be used\nfor two methodologically overlapping but distinct purposes.\nFirst, the prior to any genetic or genomic evaluation,\nevaluation of relative detection power of pedigrees, can direct\nrecruitment efforts by showing which individuals not yet\nsampled would be the most meaningful additions to a study.\nSecond, after sequencing and analysis, variants based on\nassociation with disease status and familial relationships of\nindividuals, aids in variant prioritization. Methodology is\ndescribed in Nugent (2025) .", "License": "MIT + file LICENSE", "URL": "https://github.com/SequenceBio/KinformR", "BugReports": "https://github.com/SequenceBio/KinformR/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Repository": "https://sequencebio.r-universe.dev", "Date/Publication": "2026-02-17 19:37:44 UTC", "RemoteUrl": "https://github.com/sequencebio/kinformr", "RemoteRef": "HEAD", "RemoteSha": "f1846392469c763d87305fb82cba41282ee688bf", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-19 07:42:04 UTC", "User": "root" }, "Author": "Cameron M. 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Nugent", "email": "cam.nugent@sequencebio.com", "login": "cnuge", "description": "Lead Bioinformatician | Sequence Bio", "uuid": 17327173, "orcid": "0000-0002-1135-2605" }, "_registered": true, "_dependencies": [ { "package": "devtools", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "sequencebio", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-24", "n": 1 }, { "week": "2025-26", "n": 1 }, { "week": "2025-33", "n": 1 }, { "week": "2025-36", "n": 1 }, { "week": "2025-37", "n": 1 }, { "week": "2025-39", "n": 3 }, { "week": "2025-43", "n": 1 }, { "week": "2026-07", "n": 1 }, { "week": "2026-08", "n": 1 } ], "_tags": [ { "name": "0.1.0", "date": "2025-06-12" }, { "name": "0.1.1", "date": "2025-09-24" }, { "name": "0.1.2", "date": "2026-02-17" } ], "_topics": [ "bioinformatics", "genetics", "genomics", "pedigree-analysis" ], "_stars": 1, "_contributors": [ { "user": "cnuge", "count": 88, "uuid": 17327173 } ], "_userbio": { "uuid": 22615727, "type": "organization", "name": "Sequence Bio" }, "_downloads": { "count": 150, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/KinformR" }, "_devurl": "https://github.com/sequencebio/kinformr", "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/KinformR.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/sequencebio/kinformr", "_realowner": "sequencebio", "_cranurl": true, "_releases": [ { "version": "0.1.2", "date": "2026-02-17" } ], "_exports": [ "add.fam.scores", "assign.status", "build.relation.dict", "calc.rv.score", "encode.rows", "ibd", "penetrance", "read.indiv", "read.pedigree", "read.relation.mat", "read.var.table", "score", "score.fam", "score.pedigree", "score.variant.status" ], "_help": [ { "page": "add.fam.scores", "title": "Sum all the given scores and return a single vector with cumulative \"score\", \"for\" and \"against\" vals. For use in instances where one wishes to combine scores from multiple families.", "topics": [ "add.fam.scores" ] }, { "page": "assign.a", "title": "For affecteds: Take genetic variant and determine the category of the combo.", "topics": [ "assign.a" ] }, { "page": "assign.status", "title": "Take a disease status and a genetic variant and determine which category the combo falls in. A.c = Affected individual with ALT variant A.i = Affected individual without ALT variant U.c = Unaffected individual without ALT variant U.i = Unaffected individual with ALT variant If theoretical.max = TRUE the true variant statuses are ignored and all affected/unaffected are assigned A.c and U.c respectively. These encoding can then be used show what a family's max score would be.", "topics": [ "assign.status" ] }, { "page": "assign.u", "title": "For unaffecteds: Take a genetic variant and determine the category of the combo.", "topics": [ "assign.u" ] }, { "page": "build.relation.dict", "title": "Build dictionary with the relationships falling in the different categories for the query row.", "topics": [ "build.relation.dict" ] }, { "page": "calc.rv.score", "title": "Calculate a relatedness-weighted score for a given rare variant.", "topics": [ "calc.rv.score" ] }, { "page": "encode.rows", "title": "Take the relationship matrix and the encoded statuses of info. For each row, generate the encoded data for scoring.", "topics": [ "encode.rows" ] }, { "page": "ibd", "title": "Calculation of Identity by descent (IBD).", "topics": [ "ibd" ] }, { "page": "penetrance", "title": "Likelihood function for calculation of Pedigree-based autosomal dominant penetrance value. Formula deployed via optimize so as to determine the optimal value.", "topics": [ "penetrance" ] }, { "page": "read.indiv", "title": "Read in variant and status info for individuals.", "topics": [ "read.indiv" ] }, { "page": "read.pedigree", "title": "Read in the encoded pedigree data file.", "topics": [ "read.pedigree" ] }, { "page": "read.relation.mat", "title": "Read in relationship matrix Apply the individual names to the rows and columns.", "topics": [ "read.relation.mat" ] }, { "page": "read.var.table", "title": "Read in a vcf-like subset of information obtained from use of seqbiopy's vcf_extract function on a vcf with the status encoded in the indivudal's names", "topics": [ "read.var.table" ] }, { "page": "score", "title": "Score the pedigrees using the pihat values.", "topics": [ "score" ] }, { "page": "score.fam", "title": "Given a relationship matrix and status dataframe, score a family by applying the calc.rv.score scoring system to every pairwise combination of individuals.", "topics": [ "score.fam" ] }, { "page": "score.pedigree", "title": "Take the encoded information about the pedigrees and calculate penetrance.", "topics": [ "score.pedigree" ] }, { "page": "score.variant.status", "title": "Take the dataframe with variants and status and determine which indivudals are scored correctly and which are scored incorrectly. Assign an A.c, A.i, U.c, U.i, unk", "topics": [ "score.variant.status" ] }, { "page": "subset.mat", "title": "Take the matrix and subset out only the encoded individuals that are present in the status dataframe.", "topics": [ "subset.mat" ] } ], "_readme": "https://github.com/sequencebio/kinformr/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "KinformR-penetrance_and_ibd.Rmd", "filename": "KinformR-penetrance_and_ibd.html", "title": "KinformR - penetrance and idb informed scoring of families", "author": "Cameron M. Nugent", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Estimating power of families", "Load the library", "The input data", "Simplified summary of pedigrees", "Encoding categories of relationships", "Theoretical vs. current rankings", "Note on a few special cases" ], "created": "2025-06-12 16:49:58", "modified": "2025-09-09 13:32:12", "commits": 3 }, { "source": "KinformR-variant_scoring.Rmd", "filename": "KinformR-variant_scoring.html", "title": "KinformR - pedigree-informed rare variant association scoring", "author": "Cameron M. Nugent", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Load the library", "Input data", "The relation matrix", "The status file", "Scoring a family", "How scoring works", "A Minimal example, scoring a variant from perspective of a single individual." ], "created": "2025-06-12 16:49:58", "modified": "2025-09-09 13:32:12", "commits": 3 } ], "_score": 4.954242509439325, "_indexed": true, "_nocasepkg": "kinformr", "_universes": [ "sequencebio", "cnuge" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.2", "date": "2026-05-19T07:44:17.000Z", "distro": "noble", "commit": "f1846392469c763d87305fb82cba41282ee688bf", "fileid": "c3f1ed6c198d588fe9ffbfa484a6f94bbdb7fd20deacfa82237eb8393ffab7f5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sequencebio/actions/runs/26083324802" }, { "r": "4.6.0", "os": "linux", "version": "0.1.2", "date": "2026-05-19T07:44:30.000Z", "distro": "noble", "commit": "f1846392469c763d87305fb82cba41282ee688bf", "fileid": "98b5e6ab07f59b6bbecdcf15e1884266777ee8c90350051989242004628f185f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sequencebio/actions/runs/26083324802" }, { "r": "4.5.3", "os": "mac", "version": "0.1.2", "date": "2026-05-19T07:44:26.000Z", "commit": "f1846392469c763d87305fb82cba41282ee688bf", "fileid": "acb0a1a0347a7077e639479d8d4fe8f50a68e1058a34507748dd34694831062d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sequencebio/actions/runs/26083324802" }, { "r": "4.6.0", "os": "mac", "version": "0.1.2", "date": "2026-05-19T07:43:53.000Z", "commit": "f1846392469c763d87305fb82cba41282ee688bf", "fileid": "c938ca72dda850190bd1f59c6dfab4431bf77399133f222e764519091b9bd680", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sequencebio/actions/runs/26083324802" }, { "r": "4.7.0", "os": "win", "version": "0.1.2", "date": "2026-05-19T07:43:23.000Z", "commit": "f1846392469c763d87305fb82cba41282ee688bf", "fileid": "91b68f5607e9ab357755b19223bc2a79071c2c7768b97b9ebeb653454ff77591", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sequencebio/actions/runs/26083324802" }, { "r": "4.5.3", "os": "win", "version": "0.1.2", "date": "2026-05-19T07:43:31.000Z", "commit": "f1846392469c763d87305fb82cba41282ee688bf", "fileid": "67e16ac9b6d3e4cc5895fad6311c60cd1d7a5290e76cbffaeaa8e6da82302d99", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sequencebio/actions/runs/26083324802" }, { "r": "4.6.0", "os": "win", "version": "0.1.2", "date": "2026-05-19T07:43:18.000Z", "commit": "f1846392469c763d87305fb82cba41282ee688bf", "fileid": "cbd66fc4cee1c1ec36165fa184bf0752cca0c4cf9e38f67db8ad47bee8df9ba8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sequencebio/actions/runs/26083324802" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.2", "date": "2026-06-02T15:11:54.000Z", "commit": "f1846392469c763d87305fb82cba41282ee688bf", "fileid": "8643de9ca7a78992f99db402a1c6e7bc9d1229824dba07d692e02a3f39d36fee", "status": "success", "buildurl": "https://github.com/r-universe/sequencebio/actions/runs/26083324802" } ] }