celltype_expression {SCdeconR}

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:

1. cell barcodes

2. 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.