Merge pull request #158 from jr-leary7/dev

Dev
jr-leary7 · Nov 13, 2023 · 68db088 · 68db088
2 parents 3bf18f8 + 9969206
commit 68db088
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diff --git a/.github/workflows/bioc-check.yaml b/.github/workflows/bioc-check.yaml
@@ -4,8 +4,6 @@
 on:
   push:
     branches: main
-  pull_request:
-    branches: main
 
 name: bioc-check
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -9,7 +9,6 @@ Description: This package uses truncated power basis spline models to build flex
              Downstream analysis functionalities include model comparison, dynamic gene clustering, smoothed counts generation, gene set enrichment testing, & visualization. 
 License: MIT + file LICENSE
 Encoding: UTF-8
-LazyData: true
 RoxygenNote: 7.2.1
 Depends: 
   glm2, 

diff --git a/R/clusterGenes.R b/R/clusterGenes.R
@@ -23,8 +23,9 @@
 #' @seealso \code{\link{plotClusteredGenes}}
 #' @export
 #' @examples
-#' data(sim_pseudotime)
+#' data(sim_counts)
 #' data(scLANE_models)
+#' data(sim_pseudotime)
 #' cell_offset <- createCellOffset(sim_counts)
 #' gene_clusters <- clusterGenes(scLANE_models,
 #'                               pt = sim_pseudotime,

diff --git a/R/geneProgramScoring.R b/R/geneProgramScoring.R
@@ -15,8 +15,9 @@
 #' @return Either a \code{Seurat} or \code{SingleCellExperiment} object if \code{expr.mat} is in either form, or a data.frame containing per-cell program scores if \code{expr.mat} is a matrix.
 #' @export
 #' @examples
-#' data(sim_pseudotime)
+#' data(sim_counts)
 #' data(scLANE_models)
+#' data(sim_pseudotime)
 #' smoothed_dynamics <- smoothedCountsMatrix(scLANE_models,
 #'                                           pt = sim_pseudotime,
 #'                                           n.cores = 1L)

diff --git a/man/clusterGenes.Rd b/man/clusterGenes.Rd
diff --git a/man/geneProgramScoring.Rd b/man/geneProgramScoring.Rd