sub-sub-.Seurat: Subobjects and Cell-Level Meta Data

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

Subobjects and Cell-Level Meta Data

Description

The [[ operator pulls either subobjects (eg. v3 or v5 assays, dimensional reduction information, or nearest-neighbor graphs) or cell-level meta data from a Seurat object

Usage

## S3 method for class 'Seurat'
x[[i = missing_arg(), ..., drop = FALSE, na.rm = FALSE]]

## S3 method for class 'Seurat'
head(x, n = 10L, ...)

## S3 method for class 'Seurat'
tail(x, n = 10L, ...)

Arguments

x	A Seurat object
i	Name of cell-level meta data
...	Ignored
drop	See drop
na.rm	Remove cells where meta data is all NA
n	Number of meta data rows to show

Value

Varies based on the value of i:

• If i is missing, a data frame with cell-level meta data

• If i is a vector with cell-level meta data names, a data frame (or vector of drop = TRUE) with cell-level meta data requested

• If i is a one-length character with the name of a subobject, the subobject specified by i

head: The first n rows of cell-level metadata

tail: The last n rows of cell-level metadata

See Also

See here for adding meta data with [[<-, here for adding subobjects with [[<-, and here for removing subobjects and cell-level meta data with [[<-

Seurat object, validity, and interaction methods $.Seurat(), Seurat-class, Seurat-validity, [[<-,Seurat, [[<-,Seurat,NULL, dim.Seurat(), dimnames.Seurat(), merge.Seurat(), names.Seurat(), subset.Seurat()

Examples

# Get the cell-level metadata data frame
head(pbmc_small[[]])

# Pull specific metadata information
head(pbmc_small[[c("letter.idents", "groups")]])
head(pbmc_small[["groups", drop = TRUE]])

# Get a sub-object (eg. an `Assay` or `DimReduc`)
pbmc_small[["RNA"]]
pbmc_small[["pca"]]

# Get the first 10 rows of cell-level metadata
head(pbmc_small)

# Get the last 10 rows of cell-level metadata
tail(pbmc_small)

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