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 2020-01-20.

Examples

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