Merge pull request #51 from BIMSBbioinfo/rn6

Add rn6 support

Author: retaj

R/annotate.R

@@ -10,7 +10,8 @@
 #'
 #' @export
 gtf2sqlite <-
-  function(assembly = c("hg19", "hg38", "mm10", "rn5", "dm6", "WBcel235"),
+  function(assembly = c("hg19", "hg38", "mm10", "rn5", "rn6", "dm6",
+                        "WBcel235"),
            db.file) {
 
   ah <- AnnotationHub()
@@ -105,7 +106,7 @@ setMethod("loadAnnotation", signature("character"),
 setGeneric("annotateCircs",
            function(se,
                     annot.list,
-                    assembly = c("hg19", "hg38", "mm10", "rn5", "dm6",
+                    assembly = c("hg19", "hg38", "mm10", "rn5", "rn6", "dm6",
                                  "WBcel235"),
                     fixCoordIndexing = TRUE,
                     ...)
@@ -115,7 +116,7 @@ setGeneric("annotateCircs",
 #' @rdname annotateCircs-methods
 setMethod("annotateCircs", signature("RangedSummarizedExperiment"),
           function(se, annot.list,
-                   assembly = c("hg19", "hg38", "mm10", "rn5", "dm6",
+                   assembly = c("hg19", "hg38", "mm10", "rn5", "rn6", "dm6",
                                 "WBcel235"),
                    fixCoordIndexing = TRUE, ...) {
 

R/circus.R

@@ -58,6 +58,7 @@ NULL
                            "79"      = "mar2015.archive.ensembl.org",
                            "80"      = "may2015.archive.ensembl.org",
                            "81"      = "jul2015.archive.ensembl.org",
+                           "91"      = "dec2017.archive.ensembl.org",
                            "current" = "ensembl.org"
                            ),
 
@@ -73,6 +74,7 @@ NULL
                            "mm10"     = "AH47973",
                            "dm6"      = "AH60052",
                            "rn5"      = "AH28841",
+                           "rn6"      = "AH60238",
                            "WBcel235" = "AH47942"
                            ),
 
@@ -81,6 +83,7 @@ NULL
                             "mm10"     = "current",
                             "dm6"      = "current",
                             "rn5"      = "79",
+                            "rn6"      = "91",
                             "WBcel235" = "81"
                             ),