RAMEN 2.0.0

.github/CONTRIBUTING.md

@@ -0,0 +1,106 @@
+# Contributing to RAMEN
+
+Hi there! This outlines how to propose a change to RAMEN. First of all, thanks 
+for considering contributing to our package!  It's people like you that make it 
+rewarding for us - the project maintainers - to work on RAMEN. 😊
+
+For a detailed discussion on contributing to this and other tidyverse packages, 
+please see the [development contributing guide](https://rstd.io/tidy-contrib) 
+and our [code review principles](https://code-review.tidyverse.org/).
+
+There are many ways you can contribute to this project (see  the 
+[Open Source Guide](https://opensource.guide/how-to-contribute/)). Here are some
+of them:
+
+## Engage with the package
+
+### Share the ideas
+
+Think RAMEN is useful? Let others discover it, by telling them in person, 
+via BlueSky or a blog post.
+
+Using RAMEN for a paper you are writing? Consider 
+[citing it](https://link.springer.com/article/10.1186/s13059-025-03864-4).
+
+### Ask a question
+
+Using RAMEN and got stuck? Browse the [documentation][website] to see if you 
+can find a solution. Still stuck? Post your question as an 
+[issue on GitHub][new_issue]. While we cannot offer user support, 
+we'll try to do our best to address it, as questions often lead to better 
+documentation or the discovery of bugs.
+
+Want to ask a question in private? Contact the package maintainer by 
+[email][mailto:email].
+
+### Propose an idea 💡
+
+Have an idea for a new our_package feature? Take a look at the 
+[documentation][website] and [issue list][issues] to see if it isn't included 
+or suggested yet. If not, suggest your idea as an [issue on GitHub][new_issue]. 
+While we can't promise to implement your idea, it helps to:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible.
+
+See below if you want to contribute code for your idea as well.
+
+## Improve the documentation 
+
+Noticed a typo on the website? Think a function could use a better example? 
+Good documentation makes all the difference, so your help to improve it is very welcome!
+
+You can fix typos, spelling mistakes, or grammatical errors in the 
+documentation directly using the GitHub web interface, as long as the changes 
+are made in the _source_ file.  This generally means you'll need to 
+edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in 
+an `.R`, not a `.Rd` file.  You can find the `.R` file that generates the `.Rd` 
+by reading the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and
+make sure someone from the team agrees that it’s needed. 
+
+### Report a bug
+
+Using our_package and discovered a bug? That's annoying! Don't let others have 
+the same experience and report it as well in an [issue on GitHub][new_issue] so 
+we can fix it. If you’ve found a bug, please file an issue that illustrates the 
+bug with a minimal [reprex](https://www.tidyverse.org/help/#reprex) (this will 
+also help you write a unit test, if needed).
+See our guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) 
+for more advice. Please provide as well your operating system name and version (e.g. Mac OS 10.13.6), 
+and any details about your local setup that might be helpful in troubleshooting.
+
+### Pull request process
+
+We try to follow the [GitHub flow](https://guides.github.com/introduction/flow/) for development.
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("ErickNavarroD/RAMEN", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+
+### Code style
+
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
+    You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.  
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
+   Contributions with test cases included are easier to accept.  
+
+## Code of Conduct
+
+Please note that this package is released with a [Contributor
+Code of Conduct](https://ropensci.org/code-of-conduct/). 
+By contributing to this project, you agree to abide by its terms.

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,51 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: RAMEN
 Title: RAMEN: Regional Association of Methylome variability with the Exposome and geNome
-Version: 1.0.0
+Version: 2.0.0
 Authors@R: 
     person("Erick I.", "Navarro-Delgado", , "ericknadel98@hotmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1040-3519"))
-Description: R package that identifies which genetic (G), environmental (E), additive (G+E) or interaction (GxE) model better explains DNA methylation levels in Variable Methylated Regions using microarray data.
+Description: R package that identifies which genetic (G), environmental (E), additive (G+E) or interaction (GxE) effect better explains DNA methylation levels in Variable Methylated Loci using microarray data.
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.3
 Suggests: 
     BiocStyle,
     knitr,
@@ -23,6 +23,9 @@ Imports:
     foreach,
     GenomicRanges,
     glmnet,
+    IlluminaHumanMethylation450kanno.ilmn12.hg19,
+    IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
+    IlluminaHumanMethylationEPICv2anno.20a1.hg38,
     IRanges,
     iterators,
     lifecycle,
@@ -34,6 +37,7 @@ Imports:
     tibble
 VignetteBuilder: knitr
 Depends: 
-    R (>= 2.10)
+    R (>= 4.2.0)
 LazyData: true
 URL: https://ericknavarrod.github.io/RAMEN/
+BugReports: https://github.com/ErickNavarroD/RAMEN/issues

NAMESPACE

@@ -2,12 +2,12 @@
 
 export("%>%")
 export(findCisSNPs)
-export(findVMRs)
+export(findVML)
 export(lmGE)
 export(medCorVMR)
 export(nullDistGE)
 export(selectVariables)
-export(summarizeVMRs)
+export(summarizeVML)
 importFrom(doRNG,"%dorng%")
 importFrom(foreach,"%do%")
 importFrom(foreach,"%dopar%")

NEWS.md

@@ -0,0 +1,35 @@
+# RAMEN 2.0.0
+
+In this version, we have made an important change in RAMEN terminology across all the code and documentation to more accurately reflect the biological concepts represented by the data. The term "Variably Methylated Regions (VMR)" used in RAMEN v1 has been replaced by "Variably Methylated Loci (VML)" in RAMEN v2, as not all VML are composed of 2 or more highly variable probes. VML are further composed of Variably Methylated Regions (previously named "canonical VMR" in RAMEN v1) and sparse Variably Methylated Probes (sVMPs; previously named "non-canonical VMR" in RAMENv1). To be clear, there are no changes in how these VML are identified, we only changed how we label these categories.
+
+| Updated name in RAMEN v2                | Deprecated name in RAMEN v1      |
+|---------------------------------------|---------------------------------|
+| Variably Methylated Loci (VML)          | Variably Methylated Region (VMR) |
+| Variably Methylated Region (VMR)        | canonical VMR (cVMR)             |
+| sparse Variably Methylated Probe (sVMP) | non-canonical VMR (ncVMR)        |
+
+: Terminology update
+
+-   To reflect the terminology change, the following functions had a name change: `findVML()` (previously named `findVMRs()` in RAMEN v1) and `summarizeVML()` (previously named `summarizeVMRs()` in RAMEN v1).
+
+-   `findVML()`:
+
+    -   Output: list does not separate VMRs and sVMPs into two different list elements anymore. Now, a single element ("VML") is returned in the output list, which contains both VMRs and sVMPs, labelled accordingly under the *type* column; this VML element is now a data frame, and not a Genomic Ranges object to facilitate data wrangling and plotting. The function now automatically indexes the VML.
+
+    -   The user does not need to provide the array manifest anymore if working with the Illumina 450k, EPICv1 or EPICv2 array. The `array_manifest` argument accepts now "IlluminaHumanMethylation450k", "IlluminaHumanMethylationEPICv1" and "IlluminaHumanMethylationEPICv2".
+
+    -   There is a new method to identify VML using ultrastable probes (probes which DNA methylation is known to be stable independently of tissue and developmental stage) to discriminate Highly Variable Probes, which are then grouped into VML. This method is the default one now. For more information please see the `findVML()` documentation and the package vignette. The previously default method to identify Highly Variable Probes (top 10% of probes with the highest variance in the data set) is still available using the argument `var_distribution = "all"`.
+
+-   `nullDistGE()`: Prints messages to keep track of the progress. Fixed a bug that made doFuture parallelization strategies crash.
+
+-   All functions have examples in the documentation.
+
+-   Added tests to reach a code coverage of \>90% in all functions.
+
+-   Improved error catches to make functions stop early when the inputs are not in the right format. Fixed various bugs throughout the code (no user.
+
+-   Added news, citation and contributing files to the repository.
+
+-   Citation info is provided when loading the package.
+
+-   The package repository has now informative badges and Continuous Integration checks.