metaLevels {dittoSeq}R Documentation

Gives the distinct values of a meta.data slot (or ident)

Description

Gives the distinct values of a meta.data slot (or ident)

Usage

metaLevels(meta, object, cells.use = NULL, used.only = TRUE)

Arguments

meta

quoted "meta.data.slot" name = REQUIRED. the meta.data slot whose potential values should be retrieved.

object

A target Seurat or SingleCellExperiment object

cells.use

String vector of cells'/samples' names which should be included. Alternatively, a Logical vector, the same length as the number of cells in the object, which sets which cells to include. For the typically easier logical method, provide USE in object@cell.names[USE] OR colnames(object)[USE]).

used.only

TRUE by default, whether unused levels of already

Value

Returns the distinct values of a metadata slot (factor or not) among to all cells/samples, or for a subset of cells/samples. (Alternatively, returns the distinct values of clustering if meta = "ident" and the object is a Seurat object).

Author(s)

Daniel Bunis

See Also

meta for returning an entire metadata slots of an object, not just the potential levels

getMetas for returning all metadata slots of an object

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

Examples


# dittoSeq handles bulk and single-cell data quit similarly.
# The SingleCellExperiment object structure is used for both,
# but all functions can be used similarly directly on Seurat
# objects as well.

example(importDittoBulk, echo = FALSE)

metaLevels("clustering", object = myRNA)

# Note: Set 'used.only' (default = TRUE) to FALSE to show unused levels
#  of metadata that are already factors.  By default, only the in use options
#  of a metadata are shown.
metaLevels("clustering", myRNA,
    used.only = FALSE)
[Package dittoSeq version 1.0.2 Index]