{"id":21500850,"url":"https://github.com/mcanouil/mistr","last_synced_at":"2025-07-15T22:31:59.888Z","repository":{"id":63738349,"uuid":"224893053","full_name":"mcanouil/MiSTr","owner":"mcanouil","description":"Mixed effects Score Test","archived":false,"fork":false,"pushed_at":"2022-12-05T20:24:29.000Z","size":21005,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2023-02-26T05:56:14.433Z","etag":null,"topics":["r","r-package","r-stats","rare-variant-analysis","statistics"],"latest_commit_sha":null,"homepage":"https://m.canouil.fr/MiSTr/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-2.1","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mcanouil.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-11-29T16:57:59.000Z","updated_at":"2022-03-08T10:57:05.000Z","dependencies_parsed_at":"2023-01-24T06:45:15.850Z","dependency_job_id":null,"html_url":"https://github.com/mcanouil/MiSTr","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcanouil%2FMiSTr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcanouil%2FMiSTr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcanouil%2FMiSTr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcanouil%2FMiSTr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mcanouil","download_url":"https://codeload.github.com/mcanouil/MiSTr/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":226077534,"owners_count":17570163,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["r","r-package","r-stats","rare-variant-analysis","statistics"],"created_at":"2024-11-23T17:47:58.528Z","updated_at":"2024-11-23T17:47:59.180Z","avatar_url":"https://github.com/mcanouil.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\"\n)\noptions(width = 140)\n```\n\n# *Mi*xed effects *S*core *T*est \u003cimg src=\"man/figures/mistr.png\" align=\"right\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)\n[![GitHub tag](https://img.shields.io/github/tag/mcanouil/MiSTr.svg?label=latest tag)](https://github.com/mcanouil/MiSTr)\n[![Codecov test\ncoverage](https://codecov.io/gh/mcanouil/MiSTr/branch/main/graph/badge.svg)](https://codecov.io/gh/mcanouil/MiSTr?branch=main)\n[![R-CMD-check](https://github.com/mcanouil/MiSTr/workflows/R-CMD-check/badge.svg)](https://github.com/mcanouil/MiSTr/actions)\n\u003c!-- badges: end --\u003e\n\nTest for association between a set of SNPS/genes and continuous or binary outcomes by including variant characteristic information and using (weighted) score statistics.\n\n**Note:**\n\n* From: https://cran.r-project.org/src/contrib/MiST_1.0.tar.gz\n* Reference: https://doi.org/10.1002/gepi.21717\n\n## Installation\n\n```{r}\n#| eval: false\n# Install MiSTr from CRAN:\ninstall.packages(\"MiSTr\")\n\n# Or the the development version from GitHub:\n# install.packages(\"remotes\")\nremotes::install_github(\"mcanouil/MiSTr\")\n```\n\n\n## MiSTr in Action\n\n```{r}\nlibrary(MiSTr)\ndata(mist_data)\nattach(mist_data)\n```\n\n### Continuous Outcome\n\n```{r}\nres \u003c- mist(\n  y = phenotypes[, \"y_taupi\"],\n  X = phenotypes[, paste0(\"x_cov\", 0:2)],\n  G = genotypes,\n  Z = variants_info[, 1, drop = FALSE]\n)\nstr(res)\nprint(res)\n```\n\n### Binary Outcome\n\n```{r}\nres \u003c- mist(\n  y = phenotypes[, \"y_binary\"],\n  X = phenotypes[, paste0(\"x_cov\", 0:2)],\n  G = genotypes,\n  Z = variants_info[, 1, drop = FALSE]\n)\nstr(res)\nprint(res)\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmcanouil%2Fmistr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmcanouil%2Fmistr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmcanouil%2Fmistr/lists"}