fetchData: fetchData

In fungenomics/cytobox: A toolbox for analyzing single cell RNA-seq data

Description

Subset the seurat@data matrix by gene and cluster. Similar to Seurat::FetchData except it doesn't thrown an error if a gene is not found in the data, and is more limited.

Usage

fetchData(seurat, genes, clusters = NULL, return_cell = FALSE,
  return_cluster = FALSE, scaled = FALSE)

Arguments

seurat	Seurat object
genes	Genes to filter
clusters	(Optional) Vector, include only cells with these identities (e.g. cluster assignments). Searches in seurat@ident.
return_cell	Logical, whether or not to include a column with the cell ID. Default: FALSE
return_cluster	Logical, whether or not to include a column with the cluster. Default: FALSE
scaled	Logical, whether to fetch scaled data from [e-mail]. Default: FALSE.

Value

Expression matrix for genes specified

Author(s)

Selin Jessa

Examples

fetchData(pbmc, c("IL32", "MS4A1"))
fetchData(pbmc, c("IL32"), c(1, 2))
fetchData(pbmc, c("IL32", "MS4A1"), c(1, 2), return_cluster = TRUE, return_cell = TRUE)

fungenomics/cytobox documentation built on Feb. 13, 2020, 10:51 a.m.