Merge pull request #150 from omnideconv/update_conversion_genes

Update of the conversion function

Author: LorenzoMerotto

R/mouse_deconvolution_methods.R

@@ -244,47 +244,96 @@ deconvolute_mouse <- function(gene_expression_matrix,
 
 #' This function converts the mouse gene symbols into corresponding human ones.
 #'
-#' This function relies on the `biomaRt`` package.
+#' This function relies on the `biomaRt`` package and connects to the ENSEMBL repository
+#'  to retrieve the gene symbols. If ENSEMBL cannot be reached, another solution will be
+#'  used. Since it is memory intensive, users can choose not to run it.
 #'
 #' @param gene_expression_matrix a m x n matrix with m genes and n samples.
 #'    Gene symbols must be the rownames of the matrix.
 #' @param mirror the ensembl mirror to use. Possible choices are 'www' (default),
 #'    'uswest', 'useast', 'asia'
+#' @param other_annot boolean, wether to run the other conversion method (might be memory intensive)
 #' @return the same matrix, with the counts for the corresponding human genes.
 #'    This matrix can directly be used with the immunedeconv methods. A message
 #'    will display the ratio of original genes which were converted.
 #'
 #' @export
-mouse_genes_to_human <- function(gene_expression_matrix, mirror = "www") {
+mouse_genes_to_human <- function(gene_expression_matrix, mirror = "www", other_annot = TRUE) {
   gene.names.mouse <- rownames(gene_expression_matrix)
   gene_expression_matrix$gene_name <- gene.names.mouse
 
-  # human = useMart('ensembl', dataset = 'hsapiens_gene_ensembl')
-  # mouse = useMart('ensembl', dataset = 'mmusculus_gene_ensembl')
   human <- useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl", mirror = mirror)
   mouse <- useEnsembl("ensembl", dataset = "mmusculus_gene_ensembl", mirror = mirror)
-  genes.retrieved <- getLDS(
-    attributes = c("mgi_symbol"), filters = "mgi_symbol", values = gene.names.mouse,
-    mart = mouse, attributesL = c("hgnc_symbol"), martL = human, uniqueRows = T
-  )
-
-
-  newGenes.counts <- gene_expression_matrix %>%
-    left_join(., genes.retrieved, by = c("gene_name" = "MGI.symbol")) %>%
-    select(., -c("gene_name")) %>%
-    select(., c("HGNC.symbol", everything())) %>%
-    .[!(is.na(.$HGNC.symbol)), ]
 
-  colnames(newGenes.counts)[1] <- "gene_name"
-  newGenes.counts <- newGenes.counts[!(duplicated(newGenes.counts$gene_name)), ] %>%
-    as.data.frame(.)
-  rownames(newGenes.counts) <- newGenes.counts$gene_name
-  newGenes.counts <- select(newGenes.counts, -c("gene_name"))
-
-  fraction <- 100 * (nrow(newGenes.counts) / nrow(gene_expression_matrix)) %>%
-    round(., 1)
-
-  message(paste0("ATTENTION: Only the ", fraction, "% of genes was maintained"))
+  genes.retrieved <- NULL
+  tryCatch(
+    expr = {
+      genes.retrieved <<- getLDS(
+        attributes = c("mgi_symbol"),
+        filters = "mgi_symbol", values = gene.names.mouse,
+        mart = mouse, attributesL = c("hgnc_symbol"), martL = human, uniqueRows = T
+      )
+
+      newGenes.counts <- gene_expression_matrix %>%
+        left_join(., genes.retrieved, by = c("gene_name" = "MGI.symbol")) %>%
+        select(., -c("gene_name")) %>%
+        select(., c("HGNC.symbol", everything())) %>%
+        .[!(is.na(.$HGNC.symbol)), ]
+
+      colnames(newGenes.counts)[1] <- "gene_name"
+      newGenes.counts <- newGenes.counts[!(duplicated(newGenes.counts$gene_name)), ] %>%
+        as.data.frame(.)
+      rownames(newGenes.counts) <- newGenes.counts$gene_name
+      newGenes.counts <- select(newGenes.counts, -c("gene_name"))
+
+      fraction <- 100 * (nrow(newGenes.counts) / nrow(gene_expression_matrix)) %>%
+        round(., 1)
+
+      message(paste0("ATTENTION: Only the ", fraction, "% of genes was maintained"))
+    },
+    error = function(e) {
+      print("Cannot connect to ENSEMBL. Using alternative method. This will take some time.")
+
+      if (manual_annot) {
+        # Code adapted from: https://support.bioconductor.org/p/129636/#9144606
+
+        mouse_human_genes <- read.csv("http://www.informatics.jax.org/downloads/reports/HOM_MouseHumanSequence.rpt", sep = "\t")
+
+        find_corr_gene <- function(gene, mouse_human_genes_df) {
+          class_key <- (mouse_human_genes_df %>%
+            filter(Symbol == gene & Common.Organism.Name == "mouse, laboratory"))[["DB.Class.Key"]]
+          if (!identical(class_key, integer(0))) {
+            output <- NULL
+            human_genes <- (mouse_human_genes_df %>% filter(DB.Class.Key == class_key & Common.Organism.Name == "human"))[, "Symbol"]
+            for (human_gene in human_genes) {
+              output <- append(output, human_gene)
+            }
+            if (!is.null(output)) {
+              return(
+                data.frame(
+                  "human_gene" = output,
+                  "mouse_gene" = gene
+                )
+              )
+            }
+          }
+        }
+
+        genes.retrieved <- map_dfr(gene.names.mouse, function(x) find_corr_gene(x, mouse_human_genes))
+
+        newGenes.counts <- gene_expression_matrix %>%
+          left_join(., genes.retrieved, by = c("gene_name" = "mouse_gene")) %>%
+          select(., -c("gene_name")) %>%
+          select(., c("human_gene", everything())) %>%
+          .[!(is.na(.$human_gene)), ]
+
+        fraction <- 100 * (nrow(newGenes.counts) / nrow(gene_expression_matrix)) %>%
+          round(., 1)
+
+        message(paste0("ATTENTION: Only the ", fraction, "% of genes was maintained"))
+      }
+    }
+  )
 
   return(newGenes.counts)
 }