makeTx2Gene: Make a Tx2Gene object

Description Usage Arguments Value GFF/GTF file Note Examples

Description

Make a Tx2Gene object

Usage

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makeTx2GeneFromEnsembl(
  organism,
  genomeBuild = NULL,
  release = NULL,
  ignoreVersion = TRUE
)

makeTx2GeneFromEnsDb(object, ignoreVersion = TRUE)

makeTx2GeneFromGFF(file, ignoreVersion = TRUE)

Arguments

organism

character(1). Full Latin organism name (e.g. "Homo sapiens").

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. 90). 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.

object

Object.

file

character(1). File path.

Value

Tx2Gene.

GFF/GTF file

Remote URLs and compressed files are supported.

Note

Updated 2021-03-10.

Examples

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## makeTx2GeneFromEnsembl ====
x <- makeTx2GeneFromEnsembl(organism = "Homo sapiens")
print(x)

## makeTx2GeneFromEnsDb ====
if ("EnsDb.Hsapiens.v75" %in% rownames(installed.packages())) {
    x <- makeTx2GeneFromEnsDb("EnsDb.Hsapiens.v75")
    print(x)
}

## makeTx2GeneFromGFF ====
file <- pasteURL(
    "ftp.ensembl.org",
    "pub",
    "release-102",
    "gtf",
    "homo_sapiens",
    "Homo_sapiens.GRCh38.102.gtf.gz",
    protocol = "ftp"
)
x <- makeTx2GeneFromGFF(file = file, ignoreVersion = FALSE)
print(x)

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