Add convert_ensg_to_gene function

functions.R

@@ -448,3 +448,29 @@ plotMultipleOneDimension <- function(table, pseudotimes, dir_path, colors = NULL
   }
   return(plots)
 }
+
+convert_ensg_to_gene <- function(dt) {
+  library(biomaRt)
+  mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
+  transcript_ids <- rownames(dt)
+  res <- getBM(attributes = c('ensembl_transcript_id_version', 
+                              'ensembl_gene_id', 
+                              'external_transcript_name',
+                              'external_gene_name'),
+               filters = 'external_transcript_name', 
+               values = transcript_ids,
+               mart = mart)
+
+  dt <- cbind("ensembl_transcript_id_version"=rownames(dt), dt)
+
+  library(dplyr)
+  dt <- right_join(res, dt, by = c("ensembl_transcript_id_version"="ensembl_transcript_id_version"))
+  writeTable(dt, "counts_unconcatenated.tsv")
+
+  dt <- dt[,4:ncol(dt)]
+  dt <- aggregate(. ~ external_gene_name, data=dt, FUN=sum)
+  countsTable <- dt[, 2:ncol(dt)]
+  rownames(countsTable) <- dt$external_gene_name
+  if (rownames(countsTable)[1] == ""){countsTable <- countsTable[2:nrow(countsTable),]}
+  return (countsTable)
+}