getExpressionMatrix: Get expression matrix from Seurat Object

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Get expression matrix from Seurat Object

Description

Get expression matrix from Seurat Object

Usage

getExpressionMatrix(
  so,
  only.variable = F,
  which.assay = NULL,
  which.data = "scale",
  use.additional.genes = NA,
  as.dense = F
)

Arguments

so	Seurat Object
only.variable	Logical indicating whether to include variable features only or not.
which.assay	Seurat assay to get data from. Default is DefaultAssay(so).
which.data	Specify which data to use (refers to slots in Seurat object assay). One of: "scale" - Default "data"
use.additional.genes	Character vector of additional genes to include (in addition to varibale, if variable flag is specificed). Default is NA.
as.dense	Logical to convert sparse to dense matrix. Only applies if which.data is 'data'. Default is FALSE.

Value

gene x cell expression matrix

Author(s)

Nicholas Mikolajewicz

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.