% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/seuratFunctions.R

 \name{runSeuratIntegration}
 \alias{runSeuratIntegration}
 \title{runSeuratIntegration

 A wrapper function to Seurat Batch-Correction/Integration workflow.}
 \usage{

 runSeuratIntegration(

   inSCE,
   useAssay = "counts",
   batch,
   newAssayName = "SeuratIntegratedAssay",
   kAnchor,
   kFilter,
   kWeight,
   ndims = 10
 )
 }
 \arguments{

 \item{inSCE}{Input \code{SingleCellExperiment} object that contains the assay
 to batch-correct.}

 
 \item{useAssay}{Assay to batch-correct.}
 

 \item{batch}{Batch variable from \code{colData} slot of
 \code{SingleCellExperiment} object.}

 \item{newAssayName}{Assay name for the batch-corrected output assay.}

 \item{kAnchor}{Number of neighbours to use for finding the anchors in the
 \link[Seurat]{FindIntegrationAnchors} function.}

 \item{kFilter}{Number of neighbours to use for filtering the anchors in the
 \link[Seurat]{FindIntegrationAnchors} function.}

 \item{kWeight}{Number of neighbours to use when weigthing the anchors in the
 \link[Seurat]{IntegrateData} function.}

 
 \item{ndims}{Number of dimensions to use. Default \code{10}.}
 }
 \value{

 A \code{SingleCellExperiment} object that contains the
 batch-corrected assay inside the \code{altExp} slot of the object

 }
 \description{

 runSeuratIntegration

 A wrapper function to Seurat Batch-Correction/Integration workflow.
 }