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

In dtm2451/DittoSeq: User Friendly Single-Cell and Bulk RNA Sequencing Visualization

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	optionally named string or string vector. For SummarizedExperiment or SingleCellExperiment objects, its value(s) specifies the column name of rowData(object) to be used to identify features instead of rownames(object). When targeting multiple modalities (alternative experiments), names can be used to specify which level / alternative experiment (use 'main' for the top-level) individual values should be used for. See GeneTargeting for more specifics and examples.

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)

dtm2451/DittoSeq documentation built on April 2, 2024, 8:25 p.m.