makeGRangesFromTxDb: Make GRanges from TxDb object

Description Usage Arguments Value Note Examples

View source: R/makeGRangesFromTxDb.R

Description

Make GRanges from TxDb object

Usage

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makeGRangesFromTxDb(
  object,
  level = c("transcripts", "genes", "exons", "cds"),
  ignoreVersion = TRUE,
  synonyms = FALSE
)

Arguments

object

Object.

level

character(1). Return as genes or transcripts.

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.

synonyms

logical(1). Include gene synonyms. Queries the Ensembl web server, and is CPU intensive.

Value

GRanges.

Note

Updated 2021-04-27.

Examples

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file <- pasteURL(
    "ftp.ensembl.org",
    "pub",
    "release-102",
    "gtf",
    "homo_sapiens",
    "Homo_sapiens.GRCh38.102.gtf.gz",
    protocol = "ftp"
)
txdb <- AcidGenomes::makeTxDbFromGFF(file)
gr <- makeGRangesFromTxDb(object = txdb, ignoreVersion = FALSE)
print(gr)

acidgenomics/AcidGenomes documentation built on Sept. 16, 2021, 7:30 p.m.