importTx2Gene: Import transcript-to-gene annotations

Description Usage Arguments Value Note See Also Examples

View source: R/importTx2Gene.R

Description

Generates a Tx2Gene object containing transcriptID and geneID columns.

Usage

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importTx2Gene(
  file,
  organism = NULL,
  genomeBuild = NULL,
  ensemblRelease = NULL,
  ignoreTxVersion = FALSE,
  ignoreGeneVersion = TRUE
)

Arguments

file

character(1). File path.

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").

ensemblRelease

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.

ignoreTxVersion

logical(1). Don't include the transcript version in the identifier. Not recommended by default when handing off salmon or kallisto output to tximport-DESeq2 workflow.

ignoreGeneVersion

logical(1). Don't include the gene version in the identifier. Recommended by default when handing off salmon or kallisto output to tximport-DESeq2 workflow.

Value

Tx2Gene.

Note

File should not contain column header names.

Updated 2020-05-10.

See Also

Examples

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file <- file.path(basejumpTestsURL, "tx2gene.csv")
x <- importTx2Gene(
    file = file,
    organism = "Homo sapiens",
    genomeBuild = "GRCh38",
    ensemblRelease = 90L
)
print(x)

acidgenomics/basejump documentation built on Aug. 15, 2020, 10:21 a.m.