vignette bug patch

DESCRIPTION

 Package: ViSEAGO
-Version: 1.3.13
+Version: 1.3.14
 Title: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
 Author: Aurelien Brionne [aut, cre],
         Amelie Juanchich [aut],

R/runfgsea.R

@@ -26,7 +26,7 @@
 #' @include fgsea.R
 #' @examples
 #' # gene list
-#' pregnantvslactate<-data.table::fread(
+#' PregnantvsLactate<-data.table::fread(
 #'     system.file(
 #'         "extdata/data/input",
 #'         "pregnantvslactate.complete.txt",
@@ -50,7 +50,7 @@
 #' 
 #' # run fgseaMultilevel
 #' pregnantvslactate<-ViSEAGO::runfgsea(
-#'     geneSel=pregnantvslactate,
+#'     geneSel=PregnantvsLactate,
 #'     gene2GO=myGENE2GO,
 #'     ont="BP",
 #'     method="fgseaMultilevel",

README.md

@@ -27,7 +27,7 @@ remotes::install_gitlab(
     devtools::build("ViSEAGO")
 
     # install package (from R console)
-    install.packages("ViSEAGO_1.3.13.tar.gz", repos = NULL, type = "source")
+    install.packages("ViSEAGO_1.3.14.tar.gz", repos = NULL, type = "source")
 ```
 
 ## Citation

man/runfgsea-methods.Rd

@@ -57,7 +57,7 @@ A gene frequency (\%) of leadingEdge/size is added to output \code{data.table}.
 }
 \examples{
 # gene list
-pregnantvslactate<-data.table::fread(
+PregnantvsLactate<-data.table::fread(
     system.file(
         "extdata/data/input",
         "pregnantvslactate.complete.txt",
@@ -80,7 +80,7 @@ myGENE2GO<-ViSEAGO::annotate(
 
 # run fgseaMultilevel
 pregnantvslactate<-ViSEAGO::runfgsea(
-    geneSel=pregnantvslactate,
+    geneSel=PregnantvsLactate,
     gene2GO=myGENE2GO,
     ont="BP",
     method="fgseaMultilevel",

vignettes/ViSEAGO.Rmd

@@ -53,9 +53,11 @@ BiocManager::install("ViSEAGO")
 
 # Genes of interest
 
+## topGO{-}
+
 Firstly, you need to provide the gene *background* (= expressed genes) and *selection* files.
 
-```{r geneList_input}
+```{r geneList_input_topGO}
 # load genes background
 background<-scan(
     "background.txt",
@@ -71,6 +73,18 @@ selection<-scan(
 )
 ```
 
+## fgsea{-}
+
+Or a table with gene identifiers and statistical value to use for ranking.
+
+```{r geneList_input_fgsea}
+# load gene identifiers column 1) and corresponding statistical value (column 2)
+table<-data.table::fread("table.txt")
+
+# rank gene identifiers according statistical value
+data.table::setorder(table,value)
+```
+
 # GO annotation of genes
 
 The [Gene Ontology](http://www.geneontology.org) (GO) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge @pmid25428369.