seurat_extract: Extract Data From A Seurat Object

In jackbibby1/SCPA: Single Cell Pathway Analysis

Extract Data From A Seurat Object

Description

This function takes a Seurat object as an input, and returns an expression matrix based on subsetting parameters. Either none, one, or two metadata features can be selected for a given input.

Usage

seurat_extract(
  seu_obj,
  assay = "RNA",
  meta1 = NULL,
  value_meta1 = NULL,
  meta2 = NULL,
  value_meta2 = NULL,
  pseudocount = 0.001
)

Arguments

seu_obj	Seurat object
assay	Seurat assay to extract. Defaults to RNA
meta1	Metadata column to subset
value_meta1	Value to select within meta1 column
meta2	Metadata column to subset
value_meta2	Value to select within meta2 column
pseudocount	Pseudocount to add to data. Defaults to 0.001

Value

Matrix containing count values of selected populations

Examples

## Not run: 
cd4 <- seurat_extract(
   Seurat_Object,
   meta1 = "Hour",
   value_meta1 = 12,
   meta2 = "Cell_Type",
   value_meta2 = "CD4"
)

## End(Not run)

jackbibby1/SCPA documentation built on May 14, 2024, 7:16 a.m.