diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 3d71631..9b40bf2 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -4,14 +4,19 @@ name: rworkflows branches: - master - main + - devel - RELEASE_** pull_request: branches: - master - main + - devel - RELEASE_** jobs: rworkflows: + permissions: + contents: write + packages: write runs-on: ${{ matrix.config.os }} name: ${{ matrix.config.os }} (${{ matrix.config.r }}) container: ${{ matrix.config.cont }} @@ -20,16 +25,20 @@ jobs: matrix: config: - os: ubuntu-latest - r: devel bioc: devel - cont: bioconductor/bioconductor_docker:devel - rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release + r: auto + cont: ghcr.io/bioconductor/bioconductor_docker:devel + rspm: https://packagemanager.rstudio.com/cran/__linux__/latest/release - os: macOS-latest - r: latest bioc: release + r: auto + cont: ~ + rspm: ~ - os: windows-latest - r: latest bioc: release + r: auto + cont: ~ + rspm: ~ steps: - uses: neurogenomics/rworkflows@master with: @@ -42,7 +51,7 @@ jobs: run_pkgdown: ${{ true }} has_runit: ${{ false }} has_latex: ${{ false }} - GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} run_docker: ${{ false }} DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} runner_os: ${{ runner.os }} diff --git a/R/melt_finemapping_results.R b/R/melt_finemapping_results.R deleted file mode 100644 index 2ccb9cb..0000000 --- a/R/melt_finemapping_results.R +++ /dev/null @@ -1,25 +0,0 @@ -melt_finemapping_results <- function(dat, - verbose = TRUE) { - PP_cols <- grep("\\.PP$", colnames(dat), value = TRUE) - CS_cols <- grep("\\.CS$", colnames(dat), value = TRUE) - messager("Melting PP and CS from", length(CS_cols), "fine-mapping methods", - v = verbose - ) - finemap_melt <- suppressWarnings( - data.table::melt.data.table(data.table::data.table(dat), - measure.vars = list(PP_cols, CS_cols), - variable.name = "Method", - variable.factor = TRUE, - value.name = c("PP", "CS") - ) - ) - methods_key <- setNames( - gsub("\\.PP", "", PP_cols), - unique(finemap_melt$Method) - ) - finemap_melt$Method <- factor(methods_key[finemap_melt$Method], - levels = unname(methods_key), - ordered = TRUE - ) - return(finemap_melt) -} diff --git a/README.Rmd b/README.Rmd index 1f70953..689cd32 100644 --- a/README.Rmd +++ b/README.Rmd @@ -1,12 +1,6 @@ --- title: "" -author: "

- `r badger::badge_github_version(color = 'black')` - `r badger::badge_github_actions(action = 'rworkflows')` - `r badger::badge_last_commit(branch = 'main')` - `r badger::badge_codecov(branch = 'main')` - `r badger::badge_license()` -
Author: Brian M. Schilder
" +author: "`r rworkflows::use_badges(branch='main')`" date: "
README updated: `r format( Sys.Date(), '%b-%d-%Y')`
" output: github_document diff --git a/README.md b/README.md index bbbb34f..f18167d 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,20 @@ -

-[![](https://img.shields.io/badge/devel%20version-0.99.10-black.svg)](https://github.com/RajLabMSSM/echoannot) -[![R build -status](https://github.com/RajLabMSSM/echoannot/workflows/rworkflows/badge.svg)](https://github.com/RajLabMSSM/echoannot/actions) -[![](https://img.shields.io/github/last-commit/RajLabMSSM/echoannot.svg)](https://github.com/RajLabMSSM/echoannot/commits/main) -[![](https://app.codecov.io/gh/RajLabMSSM/echoannot/branch/main/graph/badge.svg)](https://app.codecov.io/gh/RajLabMSSM/echoannot) +
[![License: GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3) -¶
¶ Author: Brian M. Schilder
-
¶ README updated: Dec-22-2022
+[![](https://img.shields.io/badge/devel%20version-0.99.11-black.svg)](https://github.com/RajLabMSSM/echoannot) +[![](https://img.shields.io/github/languages/code-size/RajLabMSSM/echoannot.svg)](https://github.com/RajLabMSSM/echoannot) +[![](https://img.shields.io/github/last-commit/RajLabMSSM/echoannot.svg)](https://github.com/RajLabMSSM/echoannot/commits/main) +
[![R build +status](https://github.com/RajLabMSSM/echoannot/workflows/rworkflows/badge.svg)](https://github.com/RajLabMSSM/echoannot/actions) +[![](https://codecov.io/gh/RajLabMSSM/echoannot/branch/main/graph/badge.svg)](https://app.codecov.io/gh/RajLabMSSM/echoannot) +
+ +

+Authors: Brian Schilder, Jack Humphrey, Towfique Raj +

+
+README updated: Oct-20-2023 +
## `echoannot`: Functions for annotating genomic data diff --git a/man/test_enrichment.Rd b/man/test_enrichment.Rd index 20fde04..02dd2eb 100644 --- a/man/test_enrichment.Rd +++ b/man/test_enrichment.Rd @@ -78,5 +78,6 @@ grlist1 <- dat[P<5e-8,] grlist2 <- dat[Support>0,] enrich <- test_enrichment(grlist1 = grlist1, grlist2 = grlist2, - ntimes = 25) + ntimes = 25, + force.parallel = FALSE) }