% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/deconvolution.R

\name{getDeconvolution}

\alias{getDeconvolution}

\title{getDeconvolution}

\usage{

getDeconvolution(

  object,

  assay = NULL,

  features = NULL,

  sc.object,

  sc.assay = "RNA",

  sc.cluster = "seurat_clusters",

  method = "RCTD",

  ...

)

}

\arguments{

\item{object}{a VoltRon object}

\item{assay}{assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \link{SampleMetadata}. 

if NULL, the default assay will be used, see \link{vrMainAssay}.}

\item{features}{features}

\item{sc.object}{Seurat Object}

\item{sc.assay}{assay of the Seurat Object used for the single cell data reference}

\item{sc.cluster}{metadata column variable used for the single cell data reference}

\item{method}{Deconvolution method, RCTD (spot), SPOTlight (spot), MuSiC (ROI)}

\item{...}{additional parameters passed to method specific functions, e.g. RCTD, MuSiC.}

}

\description{

Calculate deconvolution of spots and ROIs

}