createscRef: Construct the mean gene expression basis matrix (B), this is...

In YingMa0107/CARD: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

Construct the mean gene expression basis matrix (B), this is the faster version

Description

Construct the mean gene expression basis matrix (B), this is the faster version

Usage

createscRef(x, ct.select = NULL, ct.varname, sample.varname = NULL)

Arguments

x	S4 class for storing data from single-cell experiments. This format is usually created by the package SingleCellExperiment with stored counts, along with the usual metadata for genes and cells.
ct.select	vector of cell type names that you are interested in to deconvolute, default as NULL. If NULL, then use all cell types provided by single cell dataset;
ct.varname	character, the name of the column in metaData that specifies the cell type annotation information
sample.varname	character,the name of the column in metaData that specifies the sample information. If NULL, we just use the whole as one sample.

Value

Return a list of basis (B) matrix

YingMa0107/CARD documentation built on Feb. 14, 2024, 12:23 p.m.