Make GRanges from EnsDb object

makeGRangesFromEnsDb(object, level = c("genes", "transcripts"),
  ignoreTxVersion = TRUE)

Arguments

object

Object.

level

character(1). Return as genes or transcripts.

ignoreTxVersion

logical(1). Don't the include the transcript version in the identifier. Only applies when level = "transcripts". This simplifies identifier matching when generating a tx2gene file.

Value

GRanges.

Details

Use specific EnsDb object as annotation source. Alternatively, can pass in an EnsDb package name as a character(1).

Note

Updated 2019-09-05.

Examples

if ("EnsDb.Hsapiens.v75" %in% rownames(installed.packages())) { x <- makeGRangesFromEnsDb("EnsDb.Hsapiens.v75") }
#> Making GRanges from EnsDb object.
#> Loading required namespace: EnsDb.Hsapiens.v75
#> - Organism: "Homo sapiens" #> - Genome build: "GRCh37" #> - Ensembl release: 75L #> - Level: "genes"
#> Defining 'broadClass' using: geneBiotype, geneName, seqnames.
#> Arranging by 'geneID'.
#> 64102 genes detected.