isGene {dittoSeq}

R Documentation

Tests if input is the name of a gene in a target object.

Description

Tests if input is the name of a gene in a target object.

Usage

isGene(
  test,
  object,
  assay = .default_assay(object),
  return.values = FALSE,
  swap.rownames = NULL
)

Arguments

test	String or vector of strings, the "potential.gene.name"(s) to check for.
object	A Seurat, SingleCellExperiment, or SummarizedExperiment object.
assay	single string or integer that sets which set of seq data inside the object to check.
return.values	Logical which sets whether the function returns a logical TRUE/FALSE versus the TRUE test values . Default = FALSE REQUIRED, unless 'DEFAULT <- "object"' has been run.
swap.rownames	String. For SummarizeedExperiment or SingleCellExperiment objects, the column name of rowData(object) to be used to identify features instead of rownames(object).

Value

Returns a logical vector indicating whether each instance in test is a rowname within the requested assay of the object. Alternatively, returns the values of test that were indeed rownames if return.values = TRUE.

Author(s)

Daniel Bunis

See Also

getGenes for returning all genes in an object

gene for obtaining the expression data of genes

Examples

example(importDittoBulk, echo = FALSE)

# To see the first 10 genes of an object of a particular assay
getGenes(myRNA, assay = "counts")[1:10]

# To see all genes of an object for the default assay that dittoSeq would use
# leave out the assay input (again, remove `head()`)
head(getGenes(myRNA))

# To test if something is a gene in an object:
isGene("gene1", object = myRNA) # TRUE
isGene("CD12345", myRNA) # FALSE

# To test if many things are genes of an object
isGene(c("gene1", "gene2", "not-a-gene", "CD12345"), myRNA)

# 'return.values' input is especially useful in these cases.
isGene(c("gene1", "gene2", "not-a-gene", "CD12345"), myRNA,
    return.values = TRUE)

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