PrepData: Prepare Data

In tallulandrews/CycleMix: Cell-Cycle using Mixture Models

Prepare Data

Description

Extract the normalized expression matrix from a variety of objects used in scRNAseq.

Usage

  prepData(obj, expr_name="logcounts", do.scale=FALSE, symbol_column="feature_symbol")

Arguments

obj	a SingleCellExperiment object or a Seurat object or a matrix/Matrix.
expr_name	name of the expression matrix to use, must be an element of assays(obj), should be at minimum library-size normalized and log-transformed. If obj is a Seurat object the "assay" from which to obtain the "data" matrix from.
do.scale	whether to mean-center and scale variance of each gene.
symbol_column	name of the column of rowData(obj) which contains HGNC gene symbols, if set to NULL uses rownames.

Details

Extracts the log normalized expression matrix from the provided object - currently supports Seurat version 5, and SingleCellExperiment objects. expr_name should be the assay name for the object, e.g. "logcounts" for SingleCellExperiment or "RNA" for Seurat.

symbol_column is either the column of the rowData (SingleCellExperiment) containing the appropriate gene symbols, or should be set to NULL to use rownames, or can be a vector of gene symbols. Duplicates are removed and these are added as the rownames of the normalized expression matrix.

Value

a "matrix" or "Matrix" of the specified log-normalized expression values with the specified gene symbols as the rownames.

Examples

	expr_mat <- prepData(Ex) # Ex = SingleCellExperiment Object

tallulandrews/CycleMix documentation built on July 3, 2025, 11:41 p.m.