From d9bfdd4d6a18820d91a482bb8001dd607c6ce2ee Mon Sep 17 00:00:00 2001
From: Nick-Eagles <nick.eagles@libd.org>
Date: Tue, 26 Nov 2024 15:09:01 -0500
Subject: [PATCH] Add myself as an author, update package date, and change
 tidyverse dependency to dplyr specifically

---
 DESCRIPTION            | 10 ++++++----
 NAMESPACE              |  2 ++
 R/select_transcripts.R | 18 ++++++++++--------
 3 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9d4781e..07c29c0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: qsvaR
 Title: Generate Quality Surrogate Variable Analysis for Degradation Correction
 Version: 1.9.1
-Date: 2024-09-16
+Date: 2024-11-26
 Authors@R: 
     c(
     person("Joshua", "Stolz", email = "jstolz80@gmail.com",
@@ -11,7 +11,9 @@ Authors@R:
 	    role = c("ctb", "cre"),
 	    comment = c(ORCID = "0000-0002-0380-9740")),
     person("Leonardo", "Collado-Torres", role = c("ctb"),
-    email = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X"))
+    email = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X")),
+    person("Nicholas J.", "Eagles", email = "nickeagles77@gmail.com",
+    role = c("aut"), comment = c(ORCID = "0000-0002-9808-5254"))
     )
 Description: The qsvaR package contains functions for removing the effect of
     degration in rna-seq data from postmortem brain tissue. The package is
@@ -37,12 +39,12 @@ Suggests:
     sessioninfo,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
-Imports: 
+Imports:
+    dplyr,
     sva,
     stats,
     ggplot2,
     rlang,
-    tidyverse,
     methods
 Depends: 
     R (>= 4.2),
diff --git a/NAMESPACE b/NAMESPACE
index efd1f82..7bbf408 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -13,6 +13,8 @@ import(SummarizedExperiment)
 import(ggplot2)
 import(rlang)
 import(tidyverse)
+importFrom(dplyr,pull)
+importFrom(dplyr,slice_head)
 importFrom(methods,is)
 importFrom(stats,cor)
 importFrom(stats,prcomp)
diff --git a/R/select_transcripts.R b/R/select_transcripts.R
index c0e36ed..ae1e6ad 100644
--- a/R/select_transcripts.R
+++ b/R/select_transcripts.R
@@ -18,6 +18,8 @@
 #'
 #' @return A `character()` with the transcript IDs.
 #' @export
+#' 
+#' @importFrom dplyr pull slice_head
 #'
 #' @examples
 #' ## Default set of transcripts associated with degradation
@@ -34,21 +36,21 @@ select_transcripts <- function(top_n = 1000, cell_component = FALSE) {
 
     non_cell_tx = union(
         qsvaR::transcripts$main_model |>
-            slice_head(n = top_n) |>
-            pull(tx),
+            dplyr::slice_head(n = top_n) |>
+            dplyr::pull(tx),
         qsvaR::transcripts$int_model |>
-            slice_head(n = top_n) |>
-            pull(tx)
+            dplyr::slice_head(n = top_n) |>
+            dplyr::pull(tx)
     )
 
     if (cell_component) {
         cell_tx = union(
             qsvaR::transcripts$cell_main_model |>
-                slice_head(n = top_n) |>
-                pull(tx),
+                dplyr::slice_head(n = top_n) |>
+                dplyr::pull(tx),
             qsvaR::transcripts$cell_int_model |>
-                slice_head(n = top_n) |>
-                pull(tx)
+                dplyr::slice_head(n = top_n) |>
+                dplyr::pull(tx)
         )
         return(union(non_cell_tx, cell_tx))
     } else {