referring to mosdef when needed

R/GeneTonic-extras.R

@@ -27,7 +27,7 @@
 #' with a set of unambiguous identifiers (e.g. ENSEMBL ids) and `gene_name`,
 #' containing e.g. HGNC-based gene symbols. This object can be constructed via
 #' the `org.eg.XX.db` packages, e.g. with convenience functions such as
-#' [pcaExplorer::get_annotation_orgdb()].
+#' [mosdef::get_annotation_orgdb()].
 #'
 #' @return A `GeneTonic`-list object, containing in its named slots the arguments
 #' specified above: `dds`, `res_de`, `res_enrich`, and `annotation_obj` - the names

R/GeneTonic.R

@@ -22,7 +22,7 @@
 #' with a set of unambiguous identifiers (e.g. ENSEMBL ids) and `gene_name`,
 #' containing e.g. HGNC-based gene symbols. This object can be constructed via
 #' the `org.eg.XX.db` packages, e.g. with convenience functions such as
-#' [pcaExplorer::get_annotation_orgdb()].
+#' [mosdef::get_annotation_orgdb()].
 #' @param gtl A `GeneTonic`-list object, containing in its slots the arguments
 #' specified above: `dds`, `res_de`, `res_enrich`, and `annotation_obj` - the names
 #' of the list _must_ be specified following the content they are expecting

R/check_inputs.R

@@ -124,7 +124,7 @@ checkup_GeneTonic <- function(dds,
     stop(
       "The provided `annotation_obj` object does not respect the format required to use in GeneTonic\n",
       "e.g. all required column names have to be present.\n",
-      "You can use e.g. `pcaExplorer::get_annotation_orgdb()` for this purpose.\n",
+      "You can use e.g. `mosdef::get_annotation_orgdb()` for this purpose.\n",
       "Required columns: ", paste(colnames_annotation_obj, collapse = ", ")
     )
   }

R/gs_shaker.R

@@ -219,7 +219,7 @@ shake_topGOtableResult <- function(obj,
                                    p_value_column = "p.value_elim") {
   if (!all(c("GO.ID", "Term", "Annotated", "Significant", "Expected", "p.value_classic") %in%
     colnames(obj))) {
-    stop("The provided object must be of in the format specified by the `pcaExplorer::topGOtable` function")
+    stop("The provided object must be of in the format specified by the `pcaExplorer::topGOtable` function or the `mosdef::run_topGO` function")
   }
 
   if (!p_value_column %in% colnames(obj)) {
@@ -232,7 +232,7 @@ shake_topGOtableResult <- function(obj,
   if (!"genes" %in% colnames(obj)) {
     stop(
       "The column `genes` is not present in the provided object and is required for properly running GeneTonic.",
-      "\nMaybe you did set `addGeneToTerms` to FALSE in the call to `pcaExplorer::topGOtable`?"
+      "\nMaybe you did set `addGeneToTerms` to FALSE in the call to `pcaExplorer::topGOtable` or to `mosdef::run_topGO`?"
     )
   }
 

vignettes/GeneTonic_manual.Rmd

@@ -166,7 +166,7 @@ head(res_macrophage_IFNg_vs_naive)
 
 3. `res_enrich`: With the DE results of the previous step, we are going to extract the vector of DE genes (via `mosdef::deresult_to_df`), as well as the list of genes to be used as background, and feed these two objects into a function that computes the functional enrichment of the DE genes.
 
-   We are going to use the ORA method implemented in `r BiocStyle::Biocpkg("topGO")`, wrapped in the function `topGOtable` available in the `r BiocStyle::Biocpkg("pcaExplorer")` package, which by default uses the `BP` ontology and the `elim` method to decorrelate the GO graph structure and deliver less redundant functional categories.
+   We are going to use the ORA method implemented in `r BiocStyle::Biocpkg("topGO")`, wrapped in the function `run_topGO` available in the `r BiocStyle::Biocpkg("mosdef")` package, which by default uses the `BP` ontology and the `elim` method to decorrelate the GO graph structure and deliver less redundant functional categories.
    You can also use as an alternative the `enrichGO` function from `r BiocStyle::Biocpkg("clusterProfiler")`.
 
 ```{r create_resenrich1, eval=TRUE}
@@ -178,12 +178,11 @@ bg_ids <- rowData(dds_macrophage)$SYMBOL[rowSums(counts(dds_macrophage)) > 0]
 ```{r create_resenrich2, eval=FALSE}
 library("topGO")
 topgoDE_macrophage_IFNg_vs_naive <-
-  pcaExplorer::topGOtable(de_symbols_IFNg_vs_naive,
-                          bg_ids,
-                          ontology = "BP",
-                          mapping = "org.Hs.eg.db",
-                          geneID = "symbol",
-                          topTablerows = 500)
+  mosdef::run_topGO(de_genes = de_symbols_IFNg_vs_naive,
+                    bg_genes = bg_ids,
+                    ontology = "BP",
+                    mapping = "org.Hs.eg.db",
+                    geneID = "symbol")
 ```
 
 ```{r load_resenrich, eval=TRUE}
@@ -213,7 +212,7 @@ anno_df <- data.frame(
   row.names = rownames(dds_macrophage)
 )
 ## alternatively:
-# anno_df <- pcaExplorer::get_annotation_orgdb(dds_macrophage, "org.Hs.eg.db", "ENSEMBL")
+# anno_df <- mosdef::get_annotation_orgdb(dds_macrophage, "org.Hs.eg.db", "ENSEMBL")
 ```