OldWhichCells: Identify cells matching certain criteria

In lambdamoses/SeuratBasics: Slimmed down version of Seurat

Description

Returns a list of cells that match a particular set of criteria such as identity class, high/low values for particular PCs, ect..

Usage

OldWhichCells(object, ...)

## S3 method for class 'Assay'
OldWhichCells(
  object,
  cells,
  subset.name = NULL,
  low.threshold = -Inf,
  high.threshold = Inf,
  accept.value = NULL,
  ...
)

## S3 method for class 'Seurat'
OldWhichCells(
  object,
  cells = NULL,
  subset.name = NULL,
  low.threshold = -Inf,
  high.threshold = Inf,
  accept.value = NULL,
  ident.keep = NULL,
  ident.remove = NULL,
  max.cells.per.ident = Inf,
  random.seed = 1,
  assay = NULL,
  ...
)

Arguments

object	An object
...	Arguments passed to other methods and FetchData
cells	Subset of cell names
subset.name	Parameter to subset on. Eg, the name of a gene, PC_1, a column name in [e-mail], etc. Any argument that can be retreived using FetchData
low.threshold	Low cutoff for the parameter (default is -Inf)
high.threshold	High cutoff for the parameter (default is Inf)
accept.value	Returns all cells with the subset name equal to this value
ident.keep	Create a cell subset based on the provided identity classes
ident.remove	Subtract out cells from these identity classes (used for filtration)
max.cells.per.ident	Can be used to downsample the data to a certain max per cell ident. Default is INF.
random.seed	Random seed for downsampling
assay	Which assay to filter on

Value

A vector of cell names

See Also

FetchData

Examples

## Not run: 
OldWhichCells(object = pbmc_small, ident.keep = 2)

## End(Not run)

lambdamoses/SeuratBasics documentation built on May 6, 2020, 9:32 a.m.