WhichCells: Extract Cells for particular identity

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Extract Cells for particular identity

Description

Extract all cell barcodes for a specific identity

Usage

## S3 method for class 'liger'
WhichCells(
  object,
  idents = NULL,
  ident_col = NULL,
  by_dataset = FALSE,
  invert = FALSE,
  ...
)

Arguments

object	LIGER object name.
idents	identities to extract cell barcodes.
ident_col	name of meta data column to use when subsetting cells by identity values. Default is NULL, which will use the objects default clustering as the ident_col.
by_dataset	logical, whether to return vector with cell barcodes for all idents in or to return list (1 entry per dataset with vector of cells) (default is FALSE; return vector).
invert	logical, invert the selection of cells (default is FALSE).
...	Arguments passed to other methods

Value

vector or list depending on by_dataset parameter

Examples

## Not run: 
# Extract cells from ident =1 in current default clustering
ident1_cells <- WhichCells(object = liger_object, idents = 1)

# Extract all cells from "stim" treatment from object
stim_cells <- WhichCells(object = liger_object, idents = "stim", ident_col = "Treatment")

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.