meta: Returns the values of a meta.data for all cells/samples

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

Returns the values of a meta.data for all cells/samples

Description

Returns the values of a meta.data for all cells/samples

Usage

meta(meta, object, adjustment = NULL, adj.fxn = NULL)

Arguments

meta	String, the name of the "metadata" slot to grab. OR "ident" to retireve the clustering of a Seurat object.
object	A Seurat, SingleCellExperiment, or SummarizedExperiment object.
adjustment	A recognized string indicating whether numeric metadata should be used directly (default) versus 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] Ignored if the target metadata is not numeric.
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

Details

Retrieves the values of a metadata slot from object, or the clustering slot if meta = "ident" and the object is a Seurat.

If adjustment or adj.fxn are provided, then these requested adjustments are applied to these values (adjustment first). Note: Alterations via adjustment are only applied when metadata is numeric, but adj.fxn alterations are applied to metadata of any type.

Lastly, outputs these values are named as the cells'/samples' names.

Value

A named vector.

Author(s)

Daniel Bunis

See Also

metaLevels for returning just the unique discrete identities that exist within a metadata slot

getMetas for returning all metadata slots of an object

isMeta for testing whether something is the name of a metadata slot

Examples

example(importDittoBulk, echo = FALSE)
meta("groups", object = myRNA)

myRNA$numbers <- seq_len(ncol(myRNA))
meta("numbers", myRNA, adjustment = "z-score")
meta("numbers", myRNA, adj.fxn = as.factor)
meta("numbers", myRNA, adj.fxn = function(x) {log2(x)})

dtm2451/DittoSeq documentation built on May 4, 2024, 7:31 a.m.