{ "_id": "6a1d3db91d7bb097a0a3ff7b", "Package": "rehh", "Authors@R": "c(person(\"Alexander\", \"Klassmann\", role = c(\"aut\", \"cre\"),\nemail = \"rehh@oneoverx.eu\"),\nperson(\"Mathieu\", \"Gautier\", role = \"aut\",\nemail = \"mathieu.gautier@inrae.fr\"),\nperson(\"Renaud\", \"Vitalis\", role = \"aut\"))", "Version": "3.2.3", "License": "GPL (>= 2)", "Title": "Searching for Footprints of Selection using 'Extended Haplotype\nHomozygosity' Based Tests", "Description": "Population genetic data such as 'Single Nucleotide\nPolymorphisms' (SNPs) is often used to identify genomic regions\nthat have been under recent natural or artificial selection and\nmight provide clues about the molecular mechanisms of\nadaptation. One approach, the concept of an 'Extended Haplotype\nHomozygosity' (EHH), introduced by (Sabeti 2002)\n, has given rise to several statistics\ndesigned for whole genome scans. The package provides functions\nto compute three of these, namely: 'iHS' (Voight 2006)\n for detecting positive or\n'Darwinian' selection within a single population as well as\n'Rsb' (Tang 2007) and\n'XP-EHH' (Sabeti 2007) , targeted at\ndifferential selection between two populations. Various\nplotting functions are included to facilitate visualization and\ninterpretation of these statistics.", "VignetteBuilder": "knitr", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-01 08:02:50 UTC", "User": "root" }, "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "URL": "https://CRAN.R-project.org/package=rehh,\nhttps://gitlab.com/oneoverx/rehh", "BugReports": "https://gitlab.com/oneoverx/rehh/-/issues", "Author": "Alexander Klassmann [aut, cre], Mathieu Gautier [aut], Renaud\nVitalis [aut]", "Maintainer": "Alexander Klassmann ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-01-30 13:00:02 UTC", "RemoteUrl": "https://github.com/cran/rehh", "RemoteRef": "HEAD", "RemoteSha": "1d1abfea3ad1fa1f73fa153b629a7b39f562ffca", "MD5sum": "8b56e504f7eaae5e06d6f9aebf98b7e9", "_user": "cran", "_type": "src", "_file": "rehh_3.2.3.tar.gz", "_fileid": "90f41a816edec4c5db3f59895027a23f813718f8f4a52009676101e8771b2e78", "_filesize": 4584843, "_sha256": 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"2013-04-26" }, { "version": "1.11", "date": "2013-08-26" }, { "version": "1.12", "date": "2015-04-07" }, { "version": "1.13", "date": "2015-05-13" }, { "version": "2.0.0", "date": "2016-08-01" }, { "version": "2.0.1", "date": "2016-10-25" }, { "version": "2.0.2", "date": "2016-11-18" }, { "version": "2.0.3", "date": "2019-02-04" }, { "version": "2.0.4", "date": "2019-02-13" }, { "version": "3.0.0", "date": "2019-07-09" }, { "version": "3.0.1", "date": "2019-07-11" }, { "version": "3.1.0", "date": "2020-03-04" }, { "version": "3.1.1", "date": "2020-06-19" }, { "version": "3.1.2", "date": "2020-07-17" }, { "version": "3.2.0", "date": "2020-11-01" }, { "version": "3.2.1", "date": "2020-11-09" }, { "version": "3.2.2", "date": "2021-09-15" }, { "version": "3.2.3", "date": "2026-01-30" } ], "_exports": [ "as.newick", "calc_candidate_regions", "calc_ehh", "calc_ehhs", "calc_furcation", "calc_haplen", "calc_pairwise_haplen", "calc_region_stats", "calc_sfs_tests", "chr.name", "data2haplohh", "distribplot", "extract_regions", "freqbinplot", "furcation", "hap.names", "haplen", "haplo", "haplohh2sweepfinder", "ies2xpehh", "ihh2ihs", "ines2rsb", "make.example.files", "manhattanplot", "mrk.names", "nhap", "nmrk", "positions", "remove.example.files", "scan_hh", "scan_hh_full", "update_haplohh" ], "_datasets": [ { "name": "haplohh_cgu_bta12", "title": "Example of an 'haplohh' object", "object": "haplohh_cgu_bta12", "file": "haplohh_cgu_bta12.RData", "class": [ "haplohh" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "rehh-package", "title": "rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests", "topics": [ "rehh-package", "rehh" ] }, { "page": "allelefurcation-class", "title": "An S4 class containing furcation trees for one allele of a focal marker", "topics": [ "allelefurcation", "allelefurcation-class" ] }, { "page": "as.newick", "title": "Convert a furcation tree into Newick format", "topics": [ "as.newick" ] }, { "page": "calc_candidate_regions", "title": "Determine candidate regions of selection", "topics": [ "calc_candidate_regions" ] }, { "page": "calc_ehh", "title": "EHH and iHH computation for a given focal marker", "topics": [ "calc_ehh", "ehh", "ehh-class" ] }, { "page": "calc_ehhs", "title": "EHHS and iES computation for a given focal marker", "topics": [ "calc_ehhs", "ehhs", "ehhs-class" ] }, { "page": "calc_furcation", "title": "calculate furcation trees around a focal marker", "topics": [ "calc_furcation" ] }, { "page": "calc_haplen", "title": "Calculate length of longest shared haplotypes around a focal marker", "topics": [ "calc_haplen" ] }, { "page": "calc_pairwise_haplen", "title": "Calculate pairwise shared haplotype length between all chromosomes", "topics": [ "calc_pairwise_haplen" ] }, { "page": "calc_region_stats", "title": "Calculate score statistics for given regions", "topics": [ "calc_region_stats" ] }, { "page": "calc_sfs_tests", "title": "Calculate site frequency spectrum test statistics", "topics": [ "calc_sfs_tests" ] }, { "page": "data2haplohh", "title": "Convert data from input file to an object of class haplohh", "topics": [ "data2haplohh" ] }, { "page": "distribplot", "title": "Plot distribution of standardized iHS, Rsb or XP-EHH values", "topics": [ "distribplot" ] }, { "page": "extract_regions", "title": "Extract regions from a scan", "topics": [ "extract_regions" ] }, { "page": "freqbinplot", "title": "Plot of unstandardized iHS within frequency bins", "topics": [ "freqbinplot" ] }, { "page": "ftree-class", "title": "An S4 class to represent a furcation tree on one side of one allele of a focal marker", "topics": [ "ftree", "ftree-class" ] }, { "page": "furcation-class", "title": "An S4 class representing the complete furcation pattern around a focal marker.", "topics": [ "furcation", "furcation-class" ] }, { "page": "haplen-class", "title": "class for haplotype length", "topics": [ "haplen", "haplen-class" ] }, { "page": "haplohh_cgu_bta12", "title": "Example of an 'haplohh' object", "topics": [ "haplohh_cgu_bta12" ] }, { "page": "haplohh-class", "title": "Class \"haplohh\"", "topics": [ "chr.name", "chr.name,", "chr.name,haplohh-method", "hap.names", "hap.names,", "hap.names,haplohh-method", "haplo", "haplo,", "haplo,haplohh-method", "haplohh-class", "mrk.names", "mrk.names,", "mrk.names,haplohh-method", "nhap", "nhap,", "nhap,haplohh-method", "nmrk", "nmrk,", "nmrk,haplohh-method", "positions", "positions,", "positions,haplohh-method" ] }, { "page": "haplohh2sweepfinder", "title": "Translate object of 'haplohh-class' into SweepFinder format", "topics": [ "haplohh2sweepfinder" ] }, { "page": "ies2xpehh", "title": "Compute XP-EHH", "topics": [ "ies2xpehh" ] }, { "page": "ihh2ihs", "title": "Compute iHS", "topics": [ "ihh2ihs" ] }, { "page": "ines2rsb", "title": "Compute Rsb", "topics": [ "ines2rsb" ] }, { "page": "make.example.files", "title": "Copy example input files into current working directory", "topics": [ "make.example.files" ] }, { "page": "manhattanplot", "title": "Manhattan plot of iHS, XP-EHH or Rsb over a genome.", "topics": [ "manhattanplot" ] }, { "page": "plot.ehh", "title": "Plot EHH around a focal marker", "topics": [ "plot.ehh" ] }, { "page": "plot.ehhs", "title": "Plot EHHS around a focal marker", "topics": [ "plot.ehhs" ] }, { "page": "plot.furcation", "title": "Plots furcation trees around a focal marker", "topics": [ "plot.furcation" ] }, { "page": "plot.haplen", "title": "Plot the length of extended haplotypes around a focal marker", "topics": [ "plot.haplen" ] }, { "page": "plot.haplohh", "title": "Plot the variants of a haplohh object", "topics": [ "plot.haplohh" ] }, { "page": "remove.example.files", "title": "Remove example files from current working directory.", "topics": [ "remove.example.files" ] }, { "page": "scan_hh", "title": "Compute iHH, iES and inES over a whole chromosome", "topics": [ "scan_hh" ] }, { "page": "scan_hh_full", "title": "Compute iHH, iES and inES over a whole chromosome without cut-offs", "topics": [ "scan_hh_full" ] }, { "page": "subset.haplohh", "title": "Subsets object of 'haplohh-class'", "topics": [ "subset.haplohh" ] }, { "page": "update_haplohh", "title": "Update object of class haplohh", "topics": [ "update_haplohh" ] } ], "_rundeps": [ "rehh.data" ], "_sysdeps": [ { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "examples.Rmd", "filename": "examples.html", "title": "Examples in detail", "author": "Alexander Klassmann", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Example data set 1", "Input", "Data files", "Input options", "Calculations and visualizations", "Visualizing the sequences", "EHH", "EHHS", "\"Genome-wide\" scan", "Furcations and haplotype length", "Example data set 2", "References" ], "created": "2019-07-09 11:00:02", "modified": "2026-01-30 13:00:02", "commits": 5 }, { "source": "rehh.Rmd", "filename": "rehh.html", "title": "Vignette for package rehh", "author": "Alexander Klassmann, Renaud Vitalis and Mathieu Gautier", "engine": "knitr::rmarkdown", "headings": [ "About the package", "Background", "Changes between versions 2.X and 3.X", "Example files", "Input files", "R objects", "Terminology", "Overview", "Data input", "Haplotype data file", "Marker information file", "Loading data files: the function data2haplohh", "Example 1: reading haplotype file in standard format", "Example 2: reading haplotype file in transposed format (SHAPEIT2--like)", "Example 3: reading haplotype file in fastPHASE output format", "Example 4: reading vcf files", "Example 5: reading ms output", "Subset data", "Computing EHH, EHHS and their \"integrals\" iHH and iES", "Definition and computation", "The (allele-specific) Extended Haplotype Homozygosity (EHH)", "The integrated EHH (iHH)", "The (site-specific) Extended Haplotype Homozygosity (EHHS)", "The integrated EHHS (iES)", "The function calc_ehh()", "The function calc_ehhs()", "The function scan_hh()", "Computing iHS, Rsb and XP-EHH", "The iHS within-population statistic", "Definition", "The function ihh2ihs()", "The Rsb pairwise population statistic", "Definition", "The function ines2rsb()", "The XP-EHH pairwise population statistic", "Definition", "The function ies2xpehh()", "Delineating regions with \"outliers\": the function calc_candidate_regions()", "Visualization of the statistics", "Un-standardized iHS: the function freqbinplot()", "Rsb vs. XP-EHH comparison", "Distribution of standardized values: the function distribplot()", "Genome wide score plots: the function manhattanplot()", "Genome wide score plots: the function manhattan() of package qqman", "Visualization of the haplotype structure", "The function plot.haplohh()", "The functions calc_furcation() and plot.furcation()", "The functions calc_haplen() and plot.haplen()", "Data considerations", "Multi-allelic markers", "Dealing with gaps", "Dealing with missing data", "Dealing with multiple markers at the same position", "Dealing with unphased data", "Dealing with unpolarized data", "Differences to the program hapbin", "About estimating homozygosity", "References" ], "created": "2016-08-01 15:35:27", "modified": "2026-01-30 13:00:02", "commits": 10 } ], "_score": 6.149588567787744, "_indexed": true, "_nocasepkg": "rehh", "_universes": [ "cran", "gitlab-oneoverx" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.2.3", "date": "2026-06-01T08:05:52.000Z", "distro": "noble", "arch": "aarch64", "commit": "1d1abfea3ad1fa1f73fa153b629a7b39f562ffca", "fileid": "6248a39cdebf4ffd3eb0580b5c0886d8105427e62ac9d2ac3bc1bd905fefcbe8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26742545053" }, { "r": "4.7.0", "os": "linux", "version": "3.2.3", "date": 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