Add GRCz11 assembly

Note that this pushes some unrelated documentation changes introduced by `devtools::build`. fixes #54
BIMSBbioinfo · Mar 30, 2020 · 5e97b55 · 5e97b55
1 parent 4415370
commit 5e97b55
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Showing 14 changed files with 77 additions and 35 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -40,4 +40,4 @@ Suggests:
     testthat,
     knitr,
     lintr
-RoxygenNote: 6.1.0
+RoxygenNote: 7.1.0
diff --git a/R/annotate.R b/R/annotate.R
@@ -11,7 +11,7 @@
 #' @export
 gtf2sqlite <-
   function(assembly = c("hg19", "hg38", "mm10", "rn5", "rn6", "dm6",
-                        "WBcel235"),
+                        "WBcel235", "GRCz11"),
            db.file) {
 
   ah <- AnnotationHub()
@@ -107,7 +107,7 @@ setGeneric("annotateCircs",
            function(se,
                     annot.list,
                     assembly = c("hg19", "hg38", "mm10", "rn5", "rn6", "dm6",
-                                 "WBcel235"),
+                                 "WBcel235", "GRCz11"),
                     fixCoordIndexing = TRUE,
                     ...)
              standardGeneric("annotateCircs"))
@@ -117,7 +117,7 @@ setGeneric("annotateCircs",
 setMethod("annotateCircs", signature("RangedSummarizedExperiment"),
           function(se, annot.list,
                    assembly = c("hg19", "hg38", "mm10", "rn5", "rn6", "dm6",
-                                "WBcel235"),
+                                "WBcel235", "GRCz11"),
                    fixCoordIndexing = TRUE, ...) {
 
             if (fixCoordIndexing == TRUE) {

diff --git a/R/circus.R b/R/circus.R
@@ -59,12 +59,14 @@ NULL
                            "80"      = "may2015.archive.ensembl.org",
                            "81"      = "jul2015.archive.ensembl.org",
                            "91"      = "dec2017.archive.ensembl.org",
+                           "99"      = "jan2020.archive.ensembl.org",
                            "current" = "ensembl.org"
                            ),
 
     ensembl.organism = list("hsa" = "hsapiens",
                             "mmu" = "mmusculus",
                             "cel" = "celegans",
+                            "dre" = "drerio",
                             "rno" = "rnorvegicus",
                             "dme" = "dmelanogaster"
                             ),
@@ -73,6 +75,7 @@ NULL
                            "hg38"     = "AH47963",
                            "mm10"     = "AH47973",
                            "dm6"      = "AH60052",
+                           "GRCz11"   = "AH79086",
                            "rn5"      = "AH28841",
                            "rn6"      = "AH60238",
                            "WBcel235" = "AH47942"
@@ -82,6 +85,7 @@ NULL
                             "hg38"     = "current",
                             "mm10"     = "current",
                             "dm6"      = "current",
+                            "GRCz11"   = "99",
                             "rn5"      = "79",
                             "rn6"      = "91",
                             "WBcel235" = "81"
@@ -91,6 +95,7 @@ NULL
                              "hg38"     = "hsa",
                              "mm10"     = "mmu",
                              "dm6"      = "dme",
+                             "GRCz11"   = "dre",
                              "WBcel235" = "cel"
                              )
 

diff --git a/README.md b/README.md
@@ -29,7 +29,7 @@ install_github("BIMSBbioinfo/ciRcus", build_vignettes=FALSE)
 
 # Using the package
 ### Build TxDb object with genomic features and save locally
-Load genomic features from Ensembl and build a database for later (re)use. Currently supported assemblies are hg19, hg38, mm10, rn5, dm6 and WBcel235. This needs to be done only once per assembly.
+Load genomic features from Ensembl and build a database for later (re)use. Currently supported assemblies are hg19, hg38, mm10, rn5, dm6, GRCz11, and WBcel235. This needs to be done only once per assembly.
 ```R
 gtf2sqlite( assembly = "hg19",
             db.file  = system.file("extdata/db/human_hg19_ens75_txdb.sqlite",

diff --git a/man/AnnotateRanges.Rd b/man/AnnotateRanges.Rd
diff --git a/man/annotPie-methods.Rd b/man/annotPie-methods.Rd
diff --git a/man/annotateCircs-methods.Rd b/man/annotateCircs-methods.Rd
diff --git a/man/bedTracks-methods.Rd b/man/bedTracks-methods.Rd
diff --git a/man/ciRcus.Rd b/man/ciRcus.Rd
diff --git a/man/getIDs.Rd b/man/getIDs.Rd
diff --git a/man/getStudiesList.Rd b/man/getStudiesList.Rd
diff --git a/man/gtf2sqlite.Rd b/man/gtf2sqlite.Rd
diff --git a/man/summarizeCircs-methods.Rd b/man/summarizeCircs-methods.Rd
diff --git a/man/writeBedTracks-methods.Rd b/man/writeBedTracks-methods.Rd