Restore mirToRanges functionality

DESCRIPTION

@@ -52,6 +52,7 @@ Suggests:
     impute,
     knitr,
     magrittr,
+    miRNAmeConverter,
     org.Hs.eg.db,
     RColorBrewer,
     readr,

NAMESPACE

@@ -34,6 +34,7 @@ export(trimColData)
 export(uniformBuilds)
 import(methods)
 importFrom(BiocBaseUtils,checkInstalled)
+importFrom(BiocBaseUtils,isCharacter)
 importFrom(BiocBaseUtils,isScalarCharacter)
 importFrom(BiocBaseUtils,isScalarNumber)
 importFrom(BiocBaseUtils,lifeCycle)

R/simplifyTCGA.R

@@ -1,7 +1,7 @@
 #' @importFrom GenomicFeatures genes
 #' @importFrom GenomeInfoDb keepStandardChromosomes seqlevelsStyle
 #' seqlevelsStyle<-
-#' @importFrom BiocBaseUtils isScalarCharacter
+#' @importFrom BiocBaseUtils isScalarCharacter isCharacter
 NULL
 
 .checkHas <-
@@ -32,7 +32,12 @@ NULL
     for (i in which(which)) {
         lookup <- FUN(rownames(x[[i]]))
         ranges <- lookup[["mapped"]]
-        rse <- x[[i]][names(ranges), ]
+        if (!is.null(mcols(ranges)[["rowIdx"]]))
+            rse <- `rownames<-`(
+                x[[i]][mcols(ranges)[["rowIdx"]], ], names(ranges)
+            )
+        else
+            rse <- x[[i]][names(ranges), ]
         # rowData not merged with mcols of RHS in `rowRanges<-` method
         mcols(ranges) <-
             S4Vectors::DataFrame(rowData(rse), S4Vectors::mcols(ranges))
@@ -60,9 +65,18 @@ NULL
 #'   `GRanges()` object with ranges of mapped symbols
 #' @keywords internal
 .makeListRanges <- function(x, gn) {
-    res <- list(unmapped = x[!x %in% names(gn)])
-    x <- x[x %in% names(gn)]
-    gn <- gn[match(x, names(gn))]
+    checkInstalled("miRNAmeConverter")
+    nc <- miRNAmeConverter::MiRNANameConverter()
+    mirna_version <-
+        miRNAmeConverter::assessVersion(nc, names(gn))[1L, "version"]
+    trout <- miRNAmeConverter::translateMiRNAName(
+        nc, x, versions = mirna_version
+    )
+    new_x <- trout[[paste0("v", mirna_version, ".0")]]
+    res <- list(unmapped = setdiff(x, trout[["input"]]))
+    rowIdx <- match(tolower(trout[["input"]]), x)
+    gn <- gn[match(new_x, names(gn))]
+    mcols(gn)[["rowIdx"]] <- rowIdx
     res[["mapped"]] <- gn
     res
 }
@@ -92,9 +106,9 @@ NULL
 #' @rdname hidden-helpers
 #' @keywords internal
 .getRangesOfMir <- function(x) {
-    stopifnot(isScalarCharacter(x))
+    stopifnot(isCharacter(x))
 
-    mirnas_gr <- .get_hsa_gff3(x)
+    mirnas_gr <- .get_hsa_gff3("hg19")
 
     miR <- mirnas_gr[
         mcols(mirnas_gr)[["type"]] %in% c("miRNA", "microRNA", "tRNA")
@@ -209,9 +223,7 @@ NULL
 #'   [`RangedSummarizedExperiment`][SummarizedExperiment::RangedSummarizedExperiment-class]
 #'   objects
 #'
-#' @author L. Waldron
-#'
-#' @md
+#' @author L. Waldron, M. Ramos
 #'
 #' @examples
 #'
@@ -275,10 +287,16 @@ symbolsToRanges <- function(obj, keep.assay = FALSE, unmapped = TRUE) {
 #'
 #' @export
 mirToRanges <- function(obj, keep.assay = FALSE, unmapped = TRUE) {
-    lifeCycle(
-        package = "TCGAutils",
-        cycle = "defunct",
-        title = "simplifyTCGA"
+    checkInstalled("Bioc.gff")
+
+    can.fix <- .isFixable(mae = obj, pattern = "^hsa")
+
+    .convertTo(
+        x = obj,
+        which = can.fix,
+        FUN = .getRangesOfMir,
+        keep = keep.assay,
+        unmap = unmapped
     )
 }