{ "_id": "6a3f7c12a319ef941449b9d5", "Package": "SNPkit", "Title": "S4 Tools for Reading and Organizing Genetic Data", "Version": "0.1.0.9000", "Authors@R": "c(person(given = \"Vinícius\",\nfamily = \"Junqueira\",\nrole = c(\"aut\", \"cre\"),\nemail = \"junqueiravinicius@hotmail.com\"),\nperson(given = \"Roberto\",\nfamily = \"Higa\",\nrole = \"aut\",\nemail = \"roberto.higa@embrapa.br\"),\nperson(given = \"Fernando Flores\",\nfamily = \"Cardoso\",\nrole = \"aut\",\nemail = \"fernando.cardoso@embrapa.br\"),\nperson(given = \"Marcos Jun Iti\",\nfamily = \"Yokoo\",\nrole = \"aut\",\nemail = \"marcos.yokoo@embrapa.br\"))", "Description": "Provides an integrated suite of tools for handling single\nnucleotide polymorphism (SNP) genotype data in large-scale\ngenetic studies. Supports importing and merging genotype files,\nperforming quality control on SNP markers and samples, and\npreparing data for downstream analyses using popular software\nsuch as 'FImpute' and 'PLINK'. Offers S4 classes and methods to\nefficiently encapsulate SNP data, along with utilities for\ngenerating genotype summary statistics and visualization.\nAdditional functionalities include anticlustering approaches\nfor batch effect control, automated script generation for\nexternal software, and streamlined workflows for large datasets\ncommonly encountered in animal and plant breeding programs.\nDesigned to facilitate reproducible and scalable SNP data\nanalyses in quantitative and statistical genetics.", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "License": "GPL-3", "URL": "https://viniciusjunqueira.github.io/SNPkit/,\nhttps://github.com/viniciusjunqueira/SNPkit", "BugReports": "https://github.com/viniciusjunqueira/SNPkit/issues", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://viniciusjunqueira.r-universe.dev", "Date/Publication": "2026-06-26 13:55:53 UTC", "RemoteUrl": "https://github.com/viniciusjunqueira/snpkit", "RemoteRef": 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"read.fimpute", "run_admixture", "runAnticlusteringPCA", "runFImpute", "saveFImpute", "saveFImputeRaw", "savePlink", "Subset", "summary" ], "_help": [ { "page": "as_snpmatrix", "title": "Convert a genotype matrix or data.frame to snpStats::SnpMatrix", "topics": [ "as_snpmatrix" ] }, { "page": "cbind_SnpMatrix", "title": "Safe cbind for SnpMatrix preserving dimnames", "topics": [ "cbind_SnpMatrix" ] }, { "page": "check.call.rate", "title": "Check SNP call rate", "topics": [ "check.call.rate" ] }, { "page": "check.ibs", "title": "Check Identity-By-State (IBS) for a genotype pair", "topics": [ "check.ibs" ] }, { "page": "check.identical.samples", "title": "Check identical samples based on distance", "topics": [ "check.identical.samples" ] }, { "page": "check.identical.samples.by.block", "title": "Check identical samples by block", "topics": [ "check.identical.samples.by.block" ] }, { "page": "check.mendelian.inconsistencies", "title": "Check Mendelian inconsistencies", "topics": [ "check.mendelian.inconsistencies" ] }, { "page": "check.mendelian.inconsistencies.pair", "title": "Check Mendelian inconsistencies for a pair", "topics": [ "check.mendelian.inconsistencies.pair" ] }, { "page": "check.sample.call.rate", "title": "Check Sample Call Rate", "topics": [ "check.sample.call.rate" ] }, { "page": "check.sample.heterozygosity", "title": "Check sample heterozygosity", "topics": [ "check.sample.heterozygosity" ] }, { "page": "check.snp.chromo", "title": "Check SNP by chromosome", "topics": [ "check.snp.chromo" ] }, { "page": "check.snp.hwe", "title": "Check SNP Hardy-Weinberg equilibrium deviation", "topics": [ "check.snp.hwe" ] }, { "page": "check.snp.hwe.chi2", "title": "Check SNPs for Hardy-Weinberg equilibrium deviation using chi-square p-values", "topics": [ "check.snp.hwe.chi2" ] }, { "page": "check.snp.maf", "title": "Check SNP minor allele frequency", "topics": [ "check.snp.maf" ] }, { "page": "check.snp.mgf", "title": "Check SNP missing genotype frequencies", "topics": [ "check.snp.mgf" ] }, { "page": "check.snp.monomorf", "title": "Check SNP monomorphic status", "topics": [ "check.snp.monomorf" ] }, { "page": "check.snp.no.position", "title": "Check SNP no position", "topics": [ "check.snp.no.position" ] }, { "page": "check.snp.same.position", "title": "Check SNPs mapped to the same position", "topics": [ "check.snp.same.position" ] }, { "page": "combineSNPData", "title": "Combine multiple SNPDataLong objects", "topics": [ "combineSNPData" ] }, { "page": "doPCA", "title": "Do genome relationship matrix PCA", "topics": [ "doPCA" ] }, { "page": "exploratory.plots", "title": "Exploratory plots for SNP and sample summary", "topics": [ "exploratory.plots" ] }, { "page": "FImputeExport-class", "title": "FImputeExport Class", "topics": [ "FImputeExport-class" ] }, { "page": "FImputeRunner", "title": "Build FImputeRunner object", "topics": [ "FImputeRunner" ] }, { "page": "FImputeRunner-class", "title": "FImputeRunner Class", 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SnpMatrix objects with differing columns", "topics": [ "rbindSnpFlexible" ] }, { "page": "read.fimpute", "title": "Read imputed genotypes from FImpute output and return SNPDataLong object", "topics": [ "read.fimpute" ] }, { "page": "run_admixture", "title": "Run ADMIXTURE analysis", "topics": [ "run_admixture" ] }, { "page": "runAnticlusteringPCA", "title": "Run PCA and anticlustering on SNPDataLong", "topics": [ "runAnticlusteringPCA" ] }, { "page": "runFImpute", "title": "Run FImpute from a FImputeRunner object", "topics": [ "runFImpute", "runFImpute,FImputeRunner-method" ] }, { "page": "saveFImpute", "title": "Save genotype and map files in FImpute format", "topics": [ "saveFImpute", "saveFImpute,FImputeExport-method", "saveFImpute,SNPDataLong-method" ] }, { "page": "saveFImputeRaw", "title": "Export genotypes and map using basic arguments", "topics": [ "saveFImputeRaw" ] }, { "page": "savePlink", "title": "Save SNPDataLong object to PLINK format", "topics": [ "savePlink" ] }, { 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