From 61e2a67e1006296296b1f8c38d1527f533b3c968 Mon Sep 17 00:00:00 2001
From: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: Sat, 21 Sep 2024 13:07:04 -0400
Subject: [PATCH] docs: add a documentation file for the `dCovid_diffexp.tsv`
 file

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
---
 DESCRIPTION                  |  2 +-
 codemeta.json                |  4 ++--
 inst/script/dCovid_diffexp.R | 19 +++++++++++++++++++
 3 files changed, 22 insertions(+), 3 deletions(-)
 create mode 100644 inst/script/dCovid_diffexp.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 09adced..e2ad358 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: drugfindR
 Title: Investigate iLINCS for candidate repurposable drugs
-Version: 0.99.986
+Version: 0.99.987
 Authors@R: c(
     person(given = c("Ali", "Sajid"),
            family = "Imami",
diff --git a/codemeta.json b/codemeta.json
index 8c53b02..3ef088c 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -7,7 +7,7 @@
   "codeRepository": "https://github.com/CogDisResLab/drugfindR",
   "issueTracker": "https://github.com/CogDisResLab/drugfindR/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.99.986",
+  "version": "0.99.987",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -350,7 +350,7 @@
   "applicationCategory": "Genomics",
   "isPartOf": "https://bioconductor.org",
   "keywords": ["LINCS", "iLINCS", "drugrepurposing", "drugdiscovery", "transcriptomics", "geneexpression", "geneknockdown", "geneoverexpression", "chemicalperturbagen", "drugfindR", "r", "ilincs", "bioinformatics", "bioinformatics-pipeline"],
-  "fileSize": "2085.479KB",
+  "fileSize": "2086.498KB",
   "releaseNotes": "https://github.com/CogDisResLab/drugfindR/blob/master/NEWS.md",
   "readme": "https://github.com/CogDisResLab/drugfindR/blob/devel/README.md",
   "contIntegration": ["https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml", "https://app.codecov.io/gh/CogDisResLab/drugfindR?branch=devel"],
diff --git a/inst/script/dCovid_diffexp.R b/inst/script/dCovid_diffexp.R
new file mode 100644
index 0000000..56bc501
--- /dev/null
+++ b/inst/script/dCovid_diffexp.R
@@ -0,0 +1,19 @@
+# This script servers as both documentation and script to downlaod
+# the data file dCovid_diffexp.tsv from Zenodo.
+#
+# This file is used in the vignette to demonstrate the use of the
+# drugfindR package.
+
+# The file that we download is part of a set of differential gene expression
+# files that are located in the Zenodo repository at the following URL:
+# https://zenodo.org/record/10265182
+# These files were generated by the author, who is also the author of the
+# publication "Identification of candidate repurposable drugs to combat COVID‑19 using a signature‑based approach" (https://doi.org/10.1038/s41598-021-84044-9).
+#
+# This particular file contains the differential gene expression data for the
+# patients with COVID-19 compared to the healthy controls.
+url  <- "https://zenodo.org/records/10265182/files/dCovid_diffexp.tsv"
+
+# We download the file to the inst/extdata directory of the package.
+location <- file.path("inst", "extdata", "dCovid_diffexp.tsv")
+download.file(url, location, method = "auto")