edit for BioC resubmission

PYangLab · Oct 11, 2021 · 1ef90bd · 1ef90bd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Cepo
 Title: Cepo for the identification of differentially stable genes
-Version: 0.99.2
+Version: 0.99.3
 Authors@R: 
     c(
     person(given = "Hani Jieun",
@@ -51,4 +51,5 @@ Suggests:
     patchwork
 VignetteBuilder: knitr
 Depends: 
+    GSEABase,
     R (>= 4.1)
diff --git a/README.Rmd b/README.Rmd
@@ -18,6 +18,14 @@ using the `remotes` package:
 remotes::install_github("PYangLab/Cepo")
 ```
 
+You can install the Bioconductor version of _Cepo_ from:
+
+``` r
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install("Cepo")
+```
+
 To also build the vignettes use:
 
 ``` r

diff --git a/man/Cepo.Rd b/man/Cepo.Rd
diff --git a/man/setCepoBPPARAM.Rd b/man/setCepoBPPARAM.Rd
diff --git a/vignettes/cepo.Rmd b/vignettes/cepo.Rmd
@@ -33,8 +33,9 @@ citation("Cepo")
 ## Package installation
 The development version of *Cepo* can be installed with the following command:
 ```
-install.packages("remotes")
-remotes::install_github("PYangLab/Cepo")
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install("Cepo")
 ```
 
 # Differential stability analysis using Cepo
@@ -255,8 +256,7 @@ library(escape)
 library(fgsea)
 hallmark <- getGeneSets(species = "Homo sapiens", 
                            library = "H")
-hallmarkList <- lapply(hallmark@.Data, function(x) x@geneIds)
-names(hallmarkList) <- lapply(hallmark@.Data, function(x) x@setName)
+hallmarkList <- geneIds(hallmark)
 
 fgseaRes <- fgsea(pathways = hallmarkList, 
                   stats    = sort(ds_res_batches$average$stats[,"beta"]),