celltype_expression: Compute cell type specific gene expression

In SCdeconR: Deconvolution of Bulk RNA-Seq Data using Single-Cell RNA-Seq Data as Reference

Compute cell type specific gene expression

Description

Compute cell type specific gene expression based on predicted cell proportions and reference data.

Usage

celltype_expression(bulk, ref, phenodata, prop, ...)

Arguments

bulk	a matrix-like object of bulk RNA-seq data with rows representing genes, columns representing samples
ref	a matrix-like object of scRNA-seq data with rows representing genes, columns representing cells.
phenodata	a data.frame with rows representing cells, columns representing cell attributes. It should at least contain the first two columns as: cell barcodes cell types
prop	a matrix-like object of cell proportion values with rows representing cell types, columns representing samples.
...	additional parameters passed to create.RCTD from spacexr.

Details

this function is inspired by cell-type specific gene expression estimation for doublet mode in spacexr. See examples from run_de.

Value

a list with length equal to number of unique cell types in phenodata. Each element in the list represents gene expression matrix for each unique cell type.

SCdeconR documentation built on May 29, 2024, 9:03 a.m.