Merge branch 'devel' into RELEASE_3_19

Conflicts: DESCRIPTION
PavlidisLab · Jul 10, 2024 · b958582 · b958582
2 parents 700974b + 5126327
commit b958582
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: gemma.R
 Title: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses
-Version: 3.0.9
+Version: 3.0.10
 Authors@R: 
     c(person(given = "Javier", family = "Castillo-Arnemann", 
              role = c("aut"), email = "[email protected]",

diff --git a/R/convenience.R b/R/convenience.R
@@ -650,6 +650,7 @@ get_dataset_object <- function(datasets,
 #' get_differential_expression_values("GSE2018")
 get_differential_expression_values <- function(dataset = NA_character_,
                                                resultSets = NA_integer_,
+                                               keepNonSpecific = FALSE,
                                                readableContrasts = FALSE,
                                                memoised = getOption("gemma.memoised", FALSE)) {
     if (is.na(dataset) == FALSE && !isEmpty(resultSets)){
@@ -677,6 +678,11 @@ get_differential_expression_values <- function(dataset = NA_character_,
             }
             warning(msg)
         }
+
+        if(!keepNonSpecific){
+            out <- out[!(grepl("|",out$GeneSymbol,fixed = TRUE) | out$GeneSymbol == ""),]
+        }
+
         if(readableContrasts){
             return(processDEcontrasts(out, x))
         } else{