removed cp util duplicates

R/bio/diffex_commons.R

@@ -69,24 +69,6 @@ get_ensembl_build <- function(){
     biomaRt::listMarts() %>% as.data.frame() %>% filter(biomart=="ensembl") %>% with(str_match(version, " ([0-9]*) ")) %>% subset(select=2)
 }
 
-guess_pathview_species <- function(gene_id){
-    an_id <-gene_id[1]
-
-   ## see http://www.genome.jp/kegg-bin/find_org_www?mode=abbr&obj=mode.map
-
-   if(str_detect(an_id, "ENSMUSG")){
-        return("mmu")
-    }else if(str_detect(an_id, "ENSDARG")){
-        return("dre")
-    }else if(str_detect(an_id, "ENSG")){
-        return("hsa")
-    }else if(str_detect(an_id, "FBgn")){
-        return("dme")
-    }else{
-        stop(paste("could not guess mart from ", an_id))
-    }
-}
-#guess_mart("ENSCAFG00000000043")
 
 getGeneInfo <- function(gene_ids){
     martName <- guess_mart(gene_ids[1])
@@ -264,39 +246,4 @@ davidAnnotationChart <- function( someGenes, ontologies=DEF_DAVID_ONTOLOGIES ){
 #    if(nrow(annoChart) >0) annoChart <-  annoChart %>%  dplyr::select(select=-Genes)
 
     return(annoChart)
-}
-
-
-
-## todo move to diffex commons
-guess_cp_species <- function(ensIds){
-    an_id <-ensIds[1]
-
-    if(str_detect(an_id, "ENSG")){
-        return("human")
-    }else if(str_detect(an_id, "ENSMUSG")){
-        return("mouse")
-    }else if(str_detect(an_id, "ENSDARG")){
-        return("zebrafish")
-    }else if(str_detect(an_id, "FBgn")){
-        return("fly")
-    }else{
-        stop(paste("could not clusterProfiler species name from ", an_id))
-    }
-}
-
-guess_anno_db <- function(ensIds){
-    an_id <-ensIds[1]
-
-    if(str_detect(an_id, "ENSG")){
-        return("org.Hs.eg.db")
-    }else if(str_detect(an_id, "ENSMUSG")){
-        return("org.Mm.eg.db")
-    }else if(str_detect(an_id, "ENSDARG")){
-        return("org.Dr.eg.db")
-    }else if(str_detect(an_id, "FBgn")){
-        return("org.Dm.eg.db")
-    }else{
-        stop(paste("could not anno db mart from ", an_id))
-    }
 }
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