Gene2Symbol: Gene-to-symbol mappings

Description Usage Arguments Value Note See Also Examples

Description

Gene-to-symbol mappings

Usage

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Gene2Symbol(object, ...)

## S4 method for signature 'DataFrame'
Gene2Symbol(object, format = c("makeUnique", "unmodified", "1:1"))

## S4 method for signature 'GRanges'
Gene2Symbol(object, format = c("makeUnique", "unmodified", "1:1"))

## S4 method for signature 'SummarizedExperiment'
Gene2Symbol(object, format = c("makeUnique", "unmodified", "1:1"))

Arguments

object

Object.

...

Additional arguments.

format

character(1). Formatting method to apply:

  • "makeUnique": Recommended. Apply make.unique() to the geneName column. Gene symbols are made unique, while the gene IDs remain unmodified.

  • "unmodified": Return geneID and geneName columns unmodified, in long format.

  • "1:1": For gene symbols that map to multiple gene IDs, select only the first annotated gene ID.

Value

Gene2Symbol.

Note

For some organisms, gene names and gene symbols do not map 1:1 (e.g. Homo sapiens and Mus musculus). Refer to the format argument here in the documentation for approaches that deal with this issue.

For the format argument, note that "long" was used instead of "unmodified" prior to v0.10.10.

Updated 2020-01-20.

See Also

makeGene2Symbol().

Examples

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data(RangedSummarizedExperiment, package = "acidtest")
rse <- RangedSummarizedExperiment

## SummarizedExperiment ====
x <- Gene2Symbol(rse)
print(x)

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