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", "1:1", "unmodified"),
  quiet = FALSE
)

## S4 method for signature 'GRanges'
Gene2Symbol(object, ...)

Arguments

object

Object.

...

Arguments pass through to DataFrame method.

format

character(1). Formatting method to apply:

  • "makeUnique": Recommended. Apply make.unique to the geneName column. Gene names are made unique, while the identifiers remain unmodified. NA gene names will be renamed to "unannotated".

  • "1:1": For gene names that map to multiple gene identifiers, select only the first annotated gene identifier. Incomplete elements with NA gene name will be removed will be removed with an internal complete.cases call.

  • "unmodified": Return geneId and geneName columns unmodified, in long format. Incomplete elements with NA gene name will be removed with an internal complete.cases call.

quiet

logical(1). Perform command quietly, suppressing messages.

Value

Gene2Symbol.

Note

For some organisms, gene identifiers and gene names 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 2021-08-10.

See Also

makeGene2Symbol().

Examples

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data(GRanges, package = "AcidTest")

## DataFrame ====
df <- DataFrame(
    "geneId" = c(
        "ENSG00000228572.7",
        "ENSG00000182378.14"
    ),
    "geneName" = c(
        "AL954722.1",
        "PLCXD1"
    )
)
x <- Gene2Symbol(df)
print(x)

## GRanges ====
object <- GRanges
x <- Gene2Symbol(object)

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