{"Package":"mmconvert","Version":"0.12","Date":"2025-05-13","Title":"Mouse Map Converter","Description":"Convert mouse genome positions between the build 39 physical map and the genetic map of Cox et al. (2009) .","Author":"Karl W Broman [aut, cre] (ORCID:\n)","Maintainer":"Karl W Broman ","Authors@R":"person(\"Karl W\", \"Broman\", role=c(\"aut\", \"cre\"),\nemail=\"broman@wisc.edu\", comment=c(ORCID = \"0000-0002-4914-6671\"))","Depends":"R (>= 3.5.0)","Imports":"Rcpp (>= 0.12.12)","Suggests":"testthat, devtools, roxygen2, qtl2","License":"GPL-3","URL":"https://github.com/rqtl/mmconvert","BugReports":"https://github.com/rqtl/mmconvert/issues","LinkingTo":"Rcpp","LazyData":"true","Encoding":"UTF-8","ByteCompile":"true","RoxygenNote":"7.2.3","NeedsCompilation":"yes","Packaged":"2025-05-13 14:15:02 UTC; kbroman","Repository":"CRAN","Date/Publication":"2025-05-13 14:40:06 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/mmconvert_0.12.tar.gz","jsonAuthors":[{"name":"Karl W Broman","email":"broman@wisc.edu","maintainer":true}],"readme":"### mmconvert\n\n[![R-CMD-check](https://github.com/rqtl/mmconvert/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rqtl/mmconvert/actions/workflows/R-CMD-check.yaml)\n[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/mmconvert)](https://cran.r-project.org/package=mmconvert)\n[![zenodo DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5565363.svg)](https://doi.org/10.5281/zenodo.5565363)\n\n[Karl Broman](https://kbroman.org)\n\nR package to convert mouse genome positions between build 39 physical locations and\nthe [Cox genetic map](https://doi.org/10.1534/genetics.109.105486) positions.\n(See the [Cox map version 3](https://github.com/kbroman/CoxMapV3), updated\nfor the build 39 physical map.)\n\nThe package is a reimplementation of part of the basic functionality\nof the mouse map converter web service from Gary Churchill's group at\nthe Jackson Lab.\n\n---\n\n### Installation\n\nInstall the package from\n[CRAN](https://cran.r-project.org/package=mmconvert) with\n`install.packages(\"mmconvert\")`.\n\nAlternatively, install the mmconvert package from\n[GitHub](https://github.com/rqtl/mmconvert) using the\n[remotes package](https://remotes.r-lib.org):\n\n install.packages(\"remotes\")\n remotes::install_github(\"rqtl/mmconvert\")\n\n---\n\n### Usage\n\n[mmconvert](https://github.com/rqtl/mmconvert) contains two functions:\n`mmconvert()` and `cross2_to_grcm39()`.\n\n#### `mmconvert()`\n\n`mmconvert()` takes a set of positions as input, plus an\nindication of whether they are basepairs or Mbp (in build 39) or\nsex-averaged, female, or male cM from a slightly smoothed version of the [revised Cox genetic\nmap](https://github.com/kbroman/CoxMapV3).\n\nThe input positions can be character strings like `\"chr:position\"`.\n\n\n```r\ninput_char <- c(rs13482072=\"14:6738536\", rs13482231=\"14:67215850\", gnf14.117.278=\"14:121955310\")\n```\n\nOr they can be a list of marker positions, separated by chromosome.\n\n\n```r\ninput_list <- list(\"14\"=c(rs13482072=6738536, rs13482231=67215850, gnf14.117.278=121955310))\n```\n\nOr they can be a data frame with chromosome IDs as the first column\nand positions as the second column. Marker names can either be in a\nthird column or included as row names.\n\n\n```r\ninput_df <- data.frame(chr=c(14,14,14),\n pos=c(6738536, 67215850, 121955310),\n marker=c(\"rs13482072\", \"rs13482231\", \"gnf14.117.278\"))\n```\n\nFor any of these cases, the output is a data frame with seven\ncolumns: marker, chromosome, sex-averaged cM, female cM, male cM,\nbasepairs, and mega-basepairs.\n\n\n```r\nlibrary(mmconvert)\nmmconvert(input_df)\n```\n\n```\n## marker chr cM_coxV3_ave cM_coxV3_female cM_coxV3_male bp_grcm39 Mbp_grcm39\n## rs13482072 rs13482072 14 0.3938878 0.4204617 0.3707116 6738536 6.738536\n## rs13482231 rs13482231 14 28.7007118 34.8398609 22.8635376 67215850 67.215850\n## gnf14.117.278 gnf14.117.278 14 59.5630160 64.5897950 55.0750080 121955310 121.955310\n```\n\nIf you want to give the input positions in Mbp rather than basepairs,\nuse the argument `input_type=\"Mbp\"`.\n\n\n```r\ninput_df$pos <- input_df$pos / 1e6\nmmconvert(input_df, input_type=\"Mbp\")\n```\n\n```\n## marker chr cM_coxV3_ave cM_coxV3_female cM_coxV3_male bp_grcm39 Mbp_grcm39\n## rs13482072 rs13482072 14 0.3938878 0.4204617 0.3707116 6738536 6.738536\n## rs13482231 rs13482231 14 28.7007118 34.8398609 22.8635376 67215850 67.215850\n## gnf14.117.278 gnf14.117.278 14 59.5630160 64.5897950 55.0750080 121955310 121.955310\n```\n\nThe input positions can also be provided in sex-averaged, female, or male cM.\nBut note that the bp or Mbp positions must be in mouse genome build\n39, and cM positions must be according to the\n[Cox Map V3](https://github.com/kbroman/CoxMapV3).\n\n#### `cross2_to_grcm39()`\n\n`cross2_to_grcm39()` takes a cross2 object from\n[R/qtl2](https://kbroman.org/qtl2/) with mouse genotype data from one\nof the MUGA arrays and converts it to mouse genome build GRCm39, by\npossibly subsetting the markers, reordering them according to the\nGRCm39 build, and plugging in GRCm39 Mbp positions and the revised Cox\ngenetic map. See for the\nMUGA array annotations and for\nthe revised Cox genetic map.\n\n\n```r\nfile <- paste0(\"https://raw.githubusercontent.com/rqtl/\",\n \"qtl2data/main/DOex/DOex.zip\")\n\nlibrary(qtl2)\nDOex <- read_cross2(file)\n\nDOex_rev <- cross2_to_grcm39(DOex)\n```\n\n---\n\n#### License\n\nLicensed under [GPL-3](https://www.r-project.org/Licenses/GPL-3).","jobInfo":{"package":"mmconvert","version":"0.12","parsingStatus":"success","parserVersion":2,"parsedAt":"2025-05-13T17:30:08+0000"}}

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