Deconvolute `scbench` object using all methods with default settings

Deconvolute bulk RNA-seq matrix using all methods with default settings

Deconvolute Seurat spatial object using all methods with default settings

Usage

# S3 method for scbench
deconvolute_all(scbench, scref, methods = deconvolution_methods(), ...)

# S3 method for matrix
deconvolute_all(bulk_data, scref, methods = deconvolution_methods(), ...)

# S3 method for Seurat
deconvolute_all(spatial_obj, scref, methods = deconvolution_methods(), ...)

Arguments

scbench: an `scbench` object already processed by `pseudobulks`
scref: an `screference` object containing references for all methods that require them
methods: a vector of strings, which methods to use. For available methods, consult `deconvolution_methods()`
...: passed to `deconvolute` for CIBERSORTx credentials
bulk_data: a count matrix of genes-by-samples

Value

an object of class `scbench`

a list with each method's deconvolution results