added more easy to use expression filter

R/bio/diffex_commons.R

@@ -35,6 +35,27 @@ guess_mart <- function(gene_id){
 #guess_mart("ENSCAFG00000000043")
 
 
+retainExprGenes <- function(df, id_col="ensembl_gene_id", ...){
+    ## allows to filter for expressed genes
+
+     exprGenes <- df %>% column2rownames(id_col) %>%
+        ## see https://github.com/hadley/dplyr/issues/497
+        #iris %>% select(., which(sapply(., is.numeric))) %>% head
+        select(., which(sapply(., is.numeric))) %>%
+        filterByExpression(...) %>%
+        rownames()
+
+#    exprGenes %>% head %>% print
+#    df %>% filter_(id_col %in% exprGenes)
+
+    ## see http://stackoverflow.com/questions/26492280/non-standard-evaluation-nse-in-dplyrs-filter-pulling-data-from-mysql
+    which_column <- get(id_col, df)
+    df %>% filter_(~ which_column %in% exprGenes)
+}
+
+
+
+
 getGeneInfo <- function(gene_ids){
     martName <- guess_mart(gene_ids[1])