gene {dittoSeq} | R Documentation |
Returns the expression values of a gene for all cells/samples
gene( gene, object, assay = .default_assay(object), slot = .default_slot(object), adjustment = NULL, adj.fxn = NULL, swap.rownames = NULL )
gene |
quoted "gene" name = REQUIRED. the gene whose expression data should be retrieved. |
object |
A Seurat, SingleCellExperiment, or SummarizedExperiment object. |
assay, slot |
single strings or integer that set which data to use.
Seurat and SingleCellExperiments deal with these differently, so be sure to check the documentation for whichever object you are using.
When not provided, these typical defaults for the provided
|
adjustment |
Should expression data be used directly (default) or should it be adjusted to be
|
adj.fxn |
A function which takes a vector (of metadata values) and returns a vector of the same length. For example, |
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 the expression values of a gene for all cells/samples.
Daniel Bunis
example(importDittoBulk, echo = FALSE) gene("gene1", object = myRNA, assay = "counts") # z-scored gene("gene1", object = myRNA, assay = "counts", adjustment = "z-score") # Log2'd gene("gene1", object = myRNA, assay = "counts", adj.fxn = function(x) {log2(x)}) # To see expression of the gene for the default assay that dittoSeq would use # leave out the assay input # (For this object, the default assay is the logcounts assay) gene("gene1", myRNA) # Seurat (raw counts) if (!requireNamespace("Seurat")) { gene("CD14", object = Seurat::pbmc, assay = "RNA", slot = "counts") }