makeGRangesFromEnsembl: Make genomic ranges ('GRanges') from Ensembl

In acidgenomics/r-acidgenomes: Acid Genomics Genome Annotations

Make genomic ranges (GRanges) from Ensembl

Description

Quickly obtain gene and transcript annotations from Ensembl using AnnotationHub and ensembldb.

Usage

makeGRangesFromEnsembl(
  organism,
  level = c("genes", "transcripts"),
  genomeBuild = NULL,
  release = NULL,
  ignoreVersion = FALSE,
  extraMcols = TRUE
)

makeGRangesFromEnsDb(
  object,
  level = c("genes", "transcripts"),
  ignoreVersion = FALSE,
  extraMcols = TRUE
)

Arguments

organism	character(1). Full Latin organism name (e.g. "Homo sapiens").
level	character(1). Return as genes or transcripts.
genomeBuild	character(1). Ensembl genome build assembly name (e.g. "GRCh38"). If set NULL, defaults to the most recent build available. Note: don't pass in UCSC build IDs (e.g. "hg38").
release	integer(1). Ensembl release version (e.g. 100). We recommend setting this value if possible, for improved reproducibility. When left unset, the latest release available via AnnotationHub/ensembldb is used. Note that the latest version available can vary, depending on the versions of AnnotationHub and ensembldb in use.
ignoreVersion	logical(1). Ignore identifier (e.g. transcript, gene) versions. When applicable, the identifier containing version numbers will be stored in txIdVersion and geneIdVersion, and the variants without versions will be stored in txId, txIdNoVersion, geneId, and geneIdNoVersion.
extraMcols	logical(1). Include extra metadata columns (e.g. "broadClass").
object	EnsDb or character(1). EnsDb object or name of specific annotation package containing a versioned EnsDb object (e.g. "EnsDb.Hsapiens.v75").

Details

Simply specify the desired organism, using the full Latin name. For example, we can obtain human annotations with ⁠Homo sapiens⁠. Optionally, specific Ensembl genome builds (e.g. GRCh38) and release versions (e.g. 87) are supported.

Under the hood, this function fetches annotations from AnnotationHub using the ensembldb package. AnnotationHub supports versioned Ensembl releases, back to version 87.

Genome build: use "GRCh38" instead of "hg38" for the genome build, since we're querying Ensembl and not UCSC.

Value

EnsemblGenes or EnsemblTranscripts.

Functions

• makeGRangesFromEnsembl(): Obtain annotations from Ensembl by querying AnnotationHub.

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

Broad class definitions

For gene and transcript annotations, a broadClass column is added, which generalizes the gene types into a smaller number of semantically-meaningful groups:

• coding.

• noncoding.

• pseudo.

• small.

• decaying.

• ig (immunoglobulin).

• tcr (T cell receptor).

• other.

GRCh37 (hg19) legacy annotations

makeGRangesFromEnsembl() supports the legacy Homo sapiens GRCh37 (release 75) build by internally querying the EnsDb.Hsapiens.v75 package. Alternatively, the corresponding GTF/GFF file can be loaded directly from GENCODE or Ensembl.

Note

Updated 2023-12-05.

See Also

• AnnotationHub.

• ensembldb.

• ensembldb::ensDbFromGff(), ensembldb::ensDbFromGtf().

Examples

## Get annotations from Ensembl via AnnotationHub query.
genes <- makeGRangesFromEnsembl(
    organism = "Homo sapiens",
    level = "genes"
)
summary(genes)
transcripts <- makeGRangesFromEnsembl(
    organism = "Homo sapiens",
    level = "transcripts"
)
summary(transcripts)

## Get annotations from specific EnsDb object or package.
## > if (goalie::isInstalled("EnsDb.Hsapiens.v75")) {
## >     genes <- makeGRangesFromEnsDb(
## >         object = "EnsDb.Hsapiens.v75",
## >         level = "genes"
## >     )
## >     summary(genes)
## > }

acidgenomics/r-acidgenomes documentation built on Jan. 12, 2024, 4:06 a.m.