gene: Returns the expression values of a gene for all cells/samples

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

Returns the expression values of a gene for all cells/samples

Description

Returns the expression values of a gene for all cells/samples

Usage

gene(
  gene,
  object,
  assay = .default_assay(object),
  slot = .default_slot(object),
  adjustment = NULL,
  adj.fxn = NULL,
  swap.rownames = NULL
)

Arguments

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 integers (SCEs and SEs) or a vector of such values that set which expression data to use. See GeneTargeting for specifics and examples – Seurat and SingleCellExperiment objects deal with these differently, and functionality additions in dittoSeq have led to some minimal divergence from the native methodologies.
adjustment	Should expression data be used directly (default) or should it be adjusted to be "z-score": scaled with the scale() function to produce a relative-to-mean z-score representation "relative.to.max": divided by the maximum expression value to give percent of max values between [0,1]
adj.fxn	A function which takes a vector (of metadata values) and returns a vector of the same length. For example, function(x) {log2(x)} or as.factor
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 the expression values of a gene for all cells/samples.

Author(s)

Daniel Bunis

Examples

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")
}

dtm2451/dittoSeq documentation built on May 5, 2024, 11:19 a.m.