@@ -14,6 +14,7 @@ export(exons)

 export(exons_to_genes)

 export(filter_methy)

 export(get_example_exons_mus_musculus)

+export(get_exons_grcm39)

 export(get_exons_hg19)

 export(get_exons_hg38)

 export(get_exons_homo_sapiens)

@@ -106,6 +106,58 @@ get_exons_mm10 <- function() {

         )

 }

+#' @rdname get_exons

+#' 

+#' @examples

+#' grcm39_exons <- get_exons_grcm39()

+#' 

+#' @export

+get_exons_grcm39 <- function() {

+    package_check(

+        c("TxDb.Mmusculus.UCSC.mm39.refGene", "org.Mm.eg.db"),

+        c("3.10.0", "3.15.0")

+    )

+

+    txdb <- TxDb.Mmusculus.UCSC.mm39.refGene::TxDb.Mmusculus.UCSC.mm39.refGene

+

+    genes <-  AnnotationDbi::keys(txdb, "GENEID")

+    exon_data <- suppressMessages(AnnotationDbi::select(

+        txdb,

+        keys = genes,

+        keytype = "GENEID",

+        columns = c(

+            "GENEID",

+            "TXID",

+            "EXONCHROM",

+            "EXONSTRAND",

+            "EXONSTART",

+            "EXONEND"

+        )

+    ))

+

+    symbols_data <- suppressMessages(AnnotationDbi::select(

+            org.Mm.eg.db::org.Mm.eg.db,

+            keys = genes,

+            keytype = "ENTREZID",

+            columns = c(

+                "SYMBOL"

+            )

+        )) %>%

+        dplyr::rename(GENEID = "ENTREZID")

+

+    dplyr::left_join(exon_data, symbols_data, by = "GENEID", multiple = "all") %>%

+        tibble::as_tibble() %>%

+        dplyr::rename(

+            gene_id = "GENEID",

+            chr = "EXONCHROM",

+            strand = "EXONSTRAND",

+            start = "EXONSTART",

+            end = "EXONEND",

+            transcript_id = "TXID",

+            symbol = "SYMBOL"

+        )

+}

+

 #' Get example exon annotations for mus musculus (mm10)

 #'

 #' This is a small subset of the exons returned by

@@ -3,12 +3,15 @@

 \name{get_exons}

 \alias{get_exons}

 \alias{get_exons_mm10}

+\alias{get_exons_grcm39}

 \alias{get_exons_hg19}

 \alias{get_exons_hg38}

 \title{Get exon annotations}

 \usage{

 get_exons_mm10()

+get_exons_grcm39()

+

 get_exons_hg19()

 get_exons_hg38()

@@ -24,6 +27,8 @@ objects.

 \examples{

 mm10_exons <- get_exons_mm10()

+grcm39_exons <- get_exons_grcm39()

+

 hg19_exons <- get_exons_hg19()

 hg38_exons <- get_exons_hg38()