FetchData: Access cellular data

In mojaveazure/seurat-object: Data Structures for Single Cell Data

Access cellular data

Description

Retrieves data (feature expression, PCA scores, metrics, etc.) for a set of cells in a Seurat object

Usage

FetchData(object, ...)

## S3 method for class 'DimReduc'
FetchData(object, vars, cells = NULL, ...)

## S3 method for class 'Seurat'
FetchData(
  object,
  vars,
  cells = NULL,
  layer = NULL,
  clean = TRUE,
  slot = deprecated(),
  ...
)

Arguments

object	An object
...	Arguments passed to other methods
vars	List of all variables to fetch, use keyword “ident” to pull identity classes
cells	Cells to collect data for (default is all cells)
layer	Layer to pull feature data for
clean	Remove cells that are missing data; choose from: “all”: consider all columns for cleaning “ident”: consider all columns except the identity class for cleaning “project”: consider all columns except the identity class for cleaning; fill missing identity values with the object's project “none”: do not clean Passing TRUE is a shortcut for “ident”; passing FALSE is a shortcut for “none”
slot	Deprecated in favor of layer

Value

A data frame with cells as rows and cellular data as columns

Examples

pc1 <- FetchData(object = pbmc_small, vars = 'PC_1')
head(x = pc1)
head(x = FetchData(object = pbmc_small, vars = c('groups', 'ident')))

mojaveazure/seurat-object documentation built on Dec. 13, 2024, 9:23 a.m.