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‎.Rbuildignore

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^mmer\.Rproj$
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^\.Rproj\.user$
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^LICENSE\.md$
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^Makefile$
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^README\.Rmd$
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^_pkgdown\.yml$
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^pkgdown$
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^docs$
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^pkgdown$
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^src/compile-runner.sh$
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^src/runner$
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^inst/profiling
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^inst/logo
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.idea
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.vscode
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^data-raw$
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^dev$
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.github

‎.github/workflows/pkgdown.yml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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release:
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types: [published]
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workflow_dispatch:
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name: pkgdown.yaml
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permissions: read-all
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jobs:
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pkgdown:
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runs-on: ubuntu-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::pkgdown, local::.
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needs: website
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- name: Build site
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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- name: Deploy to GitHub pages 🚀
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if: github.event_name != 'pull_request'
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uses: JamesIves/github-pages-deploy-action@v4.5.0
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with:
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clean: false
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branch: gh-pages
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folder: docs

‎.github/workflows/r-cmd-check.yml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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name: R-CMD-check.yaml
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permissions: read-all
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.gitignore

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# History files
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.Rhistory
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.Rapp.history
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# Session Data files
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.RData
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.RDataTmp
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# User-specific files
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.Ruserdata
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# Example code in package build process
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*-Ex.R
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# Output files from R CMD build
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/*.tar.gz
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# Output files from R CMD check
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/*.Rcheck/
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# RStudio files
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.Rproj.user/
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# produced vignettes
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vignettes/*.html
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vignettes/*.pdf
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# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
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.httr-oauth
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# knitr and R markdown default cache directories
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*_cache/
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/cache/
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# Temporary files created by R markdown
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*.utf8.md
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*.knit.md
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# R Environment Variables
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.Renviron
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# pkgdown site
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docs/
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# translation temp files
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po/*~
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# RStudio Connect folder
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rsconnect/
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.Rproj.user
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mmer.Rproj
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.idea/
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.vscode/
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.DS_Store
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docs
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# Profiling files
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src/runner
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src/runner.cpp
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src/compile-runner.sh
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Rprof.out
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inst/doc

‎DESCRIPTION

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Package: mmer
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Title: The Multimodal Marginal Epistasis Test
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Version: 0.0.1
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URL: https://github.com/lcrawlab/mmer, https://lcrawlab.github.io/mmer/
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BugReports: https://github.com/lcrawlab/mmer/issues
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Authors@R: c(
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person("Julian", "Stamp", email = "julian.d.stamp@gmail.com",
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role = c("cre", "aut"), comment = c(ORCID = "0000-0003-3014-6249")),
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person("Lorin", "Crawford", email = "lcrawford@microsoft.com",
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role = "aut", comment = c(ORCID = "0000-0003-0178-8242")))
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Description: A computationally efficient genetics method which detects
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statistical epistasis in complex traits.
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License: MIT + file LICENSE
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.2
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LinkingTo:
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BH,
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Rcpp,
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RcppEigen,
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Rhdf5lib,
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testthat
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Imports:
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dplyr,
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genio,
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logging,
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mvMAPIT,
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Rcpp,
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RcppEigen,
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tidyr
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Suggests:
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GenomicRanges,
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ggplot2,
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knitr,
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rmarkdown,
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testthat (>= 3.0.0),
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xml2
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Config/testthat/edition: 3
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SystemRequirements: GNU make
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VignetteBuilder: knitr
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Depends:
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R (>= 4.4.0)
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LazyData: true
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biocViews:
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GenomeWideAssociation,
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Epistasis,
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Genetics,
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SNP,
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LinearMixedModel
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‎LICENSE

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YEAR: 2024
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COPYRIGHT HOLDER: Julian Stamp

‎LICENSE.md

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# MIT License
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Copyright (c) 2024 mmer authors
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎Makefile

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# h/t to @jimhester and @yihui for this parse block:
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# https://github.com/yihui/knitr/blob/dc5ead7bcfc0ebd2789fe99c527c7d91afb3de4a/Makefile#L1-L4
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# Note the portability change as suggested in the manual:
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# https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Writing-portable-packages
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PKGNAME = `sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION`
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PKGVERS = `sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION`
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all: check
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build: install_deps
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R CMD build .
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check: build
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R CMD check --no-manual $(PKGNAME)_$(PKGVERS).tar.gz
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install_deps:
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Rscript \
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-e 'if (!requireNamespace("remotes")) install.packages("remotes")' \
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-e 'remotes::install_deps(dependencies = TRUE)'
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install: build
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R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
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clean:
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@rm -rf $(PKGNAME)_$(PKGVERS).tar.gz $(PKGNAME).Rcheck

‎NAMESPACE

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# Generated by roxygen2: do not edit by hand
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export(approximate_memory_requirements)
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export(create_hdf5_file)
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export(mme)
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export(read_hdf5_dataset)
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export(simulate_traits)
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export(write_hdf5_dataset)
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import(Rcpp)
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import(RcppEigen)
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import(dplyr)
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import(genio)
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import(mvMAPIT)
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importFrom(stats,pnorm)
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importFrom(tidyr,pivot_longer)
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importFrom(utils,read.delim)
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importFrom(utils,write.table)
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useDynLib(mmer)

‎NEWS.md

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# mmer 0.0.1
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* Version that was used in the publication of MME.
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‎R/RcppExports.R

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# Generated by using Rcpp::compileAttributes() -> do not edit by hand
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# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
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check_openmp <- function() {
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.Call('_mmer_check_openmp', PACKAGE = 'mmer')
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}
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count_samples <- function(filename) {
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.Call('_mmer_count_samples', PACKAGE = 'mmer', filename)
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}
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count_fam <- function(filename) {
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.Call('_mmer_count_fam', PACKAGE = 'mmer', filename)
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}
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count_snps_bim <- function(filename) {
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.Call('_mmer_count_snps_bim', PACKAGE = 'mmer', filename)
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}
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createH5File <- function(filename) {
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invisible(.Call('_mmer_createH5File', PACKAGE = 'mmer', filename))
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}
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readH5File <- function(filename, datasetName) {
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.Call('_mmer_readH5File', PACKAGE = 'mmer', filename, datasetName)
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}
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replaceH5Dataset <- function(filename, datasetName, newData) {
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invisible(.Call('_mmer_replaceH5Dataset', PACKAGE = 'mmer', filename, datasetName, newData))
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}
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mme_cpp <- function(plink_file, pheno_file, genotype_mask_file, n_randvecs, n_blocks, rand_seed, gxg_indices, n_threads, gxg_h5_dataset, ld_h5_dataset) {
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.Call('_mmer_mme_cpp', PACKAGE = 'mmer', plink_file, pheno_file, genotype_mask_file, n_randvecs, n_blocks, rand_seed, gxg_indices, n_threads, gxg_h5_dataset, ld_h5_dataset)
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}
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simulate_traits_cpp <- function(plink_file, additive_heritability, gxg_heritability, additive_snps, gxg_group_1, gxg_group_2) {
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.Call('_mmer_simulate_traits_cpp', PACKAGE = 'mmer', plink_file, additive_heritability, gxg_heritability, additive_snps, gxg_group_1, gxg_group_2)
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}
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