object_data: Function to access object data

In NCBI-Hackathons/RClusterCT: Classifier for Single-cell RNA-seq Using Cell Clusters

Function to access object data

Description

Function to access object data

Usage

object_data(object, ...)

## S3 method for class 'Seurat'
object_data(object, slot, n_genes = 1000, ...)

## S3 method for class 'SingleCellExperiment'
object_data(object, slot, ...)

Arguments

object	object after tsne or umap projections and clustering
...	additional arguments
slot	data to access
n_genes	number of genes limit for Seurat variable genes, by default 1000, set to 0 to use all variable genes (generally not recommended)

Value

expression matrix, with genes as row names, and cell types as column names

Examples

so <- so_pbmc()
mat <- object_data(
    object = so,
    slot = "data"
)
mat[1:3, 1:3]
sce <- sce_pbmc()
mat <- object_data(
    object = sce,
    slot = "data"
)
mat[1:3, 1:3]

NCBI-Hackathons/RClusterCT documentation built on Aug. 30, 2024, 2:05 a.m.