Merge branch 'main' of github.com:Hongxiang2023/YAME

.github/workflows/pages.yml

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+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Deploy Jekyll site to Pages
+
+on:
+  push:
+    branches:
+      - "main"
+    paths:
+      - "docs/**"
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: docs
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.3'
+          bundler-cache: true
+          cache-version: 0
+          working-directory: '${{ github.workspace }}/docs'
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v5
+      - name: Build with Jekyll
+        # Outputs to the './_site' directory by default
+        run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
+        env:
+          JEKYLL_ENV: production
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: "docs/_site/"
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

R/testEnrichmentFisherN.R

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+testEnrichmentFisherN <- function(
+    nD, nQ, nDQ, nU, alternative = "greater") {
+  #N_mask,N_query,N_overlap,N_universe
+  nDmQ <- nD - nDQ
+  nQmD <- nQ - nDQ
+  nUmDQ <- nU - nQ - nD + nDQ
+
+  if (alternative == "two.sided") {
+    pvg <- phyper(
+      nDQ-1, nDQ + nQmD, nUmDQ + nDmQ, nDmQ + nDQ,
+      lower.tail = FALSE, log.p = TRUE) / log(10)
+    pvl <- phyper(
+      nDQ, nDQ + nQmD, nUmDQ + nDmQ, nDmQ + nDQ,
+      lower.tail = TRUE, log.p = TRUE) / log(10)
+    log10.p.value <- pmin(pmin(pvg, pvl) + log(2), 0) / log(10)
+    ## log10.p.value <- log10(fisher.test(matrix(c(
+    ##     nDQ, nDmQ, nQmD, nUmDQ), nrow = 2))$p.value)
+  } else if (alternative == "greater") {
+    log10.p.value <- phyper(
+      nDQ-1, nDQ + nQmD, nUmDQ + nDmQ, nDmQ + nDQ,
+      lower.tail = FALSE, log.p = TRUE) / log(10)
+  } else if (alternative == "less") {
+    log10.p.value <- phyper(
+      nDQ, nDQ + nQmD, nUmDQ + nDmQ, nDmQ + nDQ,
+      lower.tail = TRUE, log.p = TRUE) / log(10)
+  } else {
+    stop("alternative must be either greater, less or two-sided.")
+  }
+
+  odds_ratio <- nDQ / nQmD / nDmQ * nUmDQ # can be NaN if 0
+  odds_ratio[odds_ratio == Inf] <- .Machine$double.xmax
+  odds_ratio[odds_ratio == 0] <- .Machine$double.xmin
+  data.frame(
+    estimate = log2(odds_ratio),
+    p.value = 10**(log10.p.value),
+    log10.p.value = log10.p.value,
+    test = "Log2(OR)",
+    nQ = nQ, nD = nD, overlap = nDQ,
+    cf_Jaccard = nDQ / (nD + nQmD),
+    cf_overlap = nDQ / pmin(nD, nQ), # Szymkiewicz–Simpson
+    cf_NPMI = (log2(nD)+log2(nQ)-2*log2(nU))/(log2(nDQ)-log2(nU))-1,
+    cf_SorensenDice = 2 * nDQ/(nD + nQ))
+}

README.md

@@ -1 +1,15 @@
 # YAME (Yet Another MEthylation tool)
+
+YAME (Yet Another MEthylation tool) is a methylation toolset designed for sequence-level DNA methylation data management. It is a command-line C program capable of performing sequence-level enrichment testing, row operations (such as merging pseudobulks), downsampling, and other related tasks with ultra fast speed.
+
+## Publication
+
+If you use YAME, kindly [cite](Coming soon):
+
+```
+David Goldberg, Hongxiang Fu, Daniel Atkins, Ethan Moyer, Wanding Zhou, KnowYourCG: supervised learning of sparse DNA methylomes.
+```
+
+## Usage and Documentation
+
+A User Guide has been created to provide detailed documentation of YAME. The guide can be found at: https://hongxiang2023.github.io/YAME/.

docs/.gitignore

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+# Not sure what a .gitignore is?
+# See: https://git-scm.com/docs/gitignore
+
+# These are directly copied from Jekyll's first-party docs on `.gitignore` files:
+# https://jekyllrb.com/tutorials/using-jekyll-with-bundler/#commit-to-source-control
+
+# Ignore the default location of the built site, and caches and metadata generated by Jekyll
+_site/
+.sass-cache/
+.jekyll-cache/
+.jekyll-metadata
+
+# Ignore folders generated by Bundler
+.bundle/
+vendor/

docs/404.html

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+---
+permalink: /404.html
+layout: default
+---
+
+<style type="text/css" media="screen">
+  .container {
+    margin: 10px auto;
+    max-width: 600px;
+    text-align: center;
+  }
+  h1 {
+    margin: 30px 0;
+    font-size: 4em;
+    line-height: 1;
+    letter-spacing: -1px;
+  }
+</style>
+
+<div class="container">
+  <h1>404</h1>
+
+  <p><strong>Page not found :(</strong></p>
+  <p>The requested page could not be found.</p>
+</div>

docs/Gemfile

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+source "https://rubygems.org"
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+gem "jekyll", "~> 4.3.4"
+# This is the default theme for new Jekyll sites. You may change this to anything you like.
+gem "minima", "~> 2.5"
+gem "just-the-docs"
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+# gem "github-pages", group: :jekyll_plugins
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  gem "jekyll-feed", "~> 0.12"
+end
+
+# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
+# and associated library.
+platforms :mingw, :x64_mingw, :mswin, :jruby do
+  gem "tzinfo", ">= 1", "< 3"
+  gem "tzinfo-data"
+end
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1", :platforms => [:mingw, :x64_mingw, :mswin]
+
+# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem
+# do not have a Java counterpart.
+gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby]