isGene {dittoSeq} | R Documentation |
Tests if input is the name of a gene in a target object.
isGene( test, object, assay = .default_assay(object), return.values = FALSE, swap.rownames = NULL )
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 |
swap.rownames |
String. For SummarizeedExperiment or SingleCellExperiment objects, the column name of rowData(object) to be used to identify features instead of rownames(object). |
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
.
Daniel Bunis
getGenes
for returning all genes in an object
gene
for obtaining the expression data of genes
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)