@@ -440,9 +440,6 @@ setMethod("celdaGridSearch",

 #'  \item celdaList object.}

 #' @param params List. List of parameters used to subset the matching celda

 #'  models in list \code{"celda_grid_search"} in \code{metadata(x)}.

-#' @param useAssay A string specifying which \code{assay}

-#'  slot to use if \code{x} is a

-#'  \linkS4class{SingleCellExperiment} object. Default "counts".

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param ... Ignored. Placeholder to prevent check warning.

@@ -479,7 +476,7 @@ setGeneric("subsetCeldaList", function(x, ...) {

 #' @export

 setMethod("subsetCeldaList",

     signature(x = "SingleCellExperiment"),

-    function(x, params, useAssay = "counts", altExpName = "featureSubset") {

+    function(x, params, altExpName = "featureSubset") {

         ## Check for bad parameter names

         if (!all(names(params) %in% colnames(runParams(x,

@@ -584,9 +581,6 @@ setMethod("subsetCeldaList",

 #'  best model as a

 #'  \code{celdaList} object or not. If \code{FALSE}, return the best model as a

 #'  corresponding celda model object.

-#' @param useAssay A string specifying which \code{assay}

-#'  slot to use if \code{x} is a

-#'  \linkS4class{SingleCellExperiment} object. Default "counts".

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param ... Ignored. Placeholder to prevent check warning.

@@ -620,8 +614,7 @@ setGeneric("selectBestModel", function(x, ...) {

 #' @importFrom data.table as.data.table

 #' @export

 setMethod("selectBestModel", signature(x = "SingleCellExperiment"),

-    function(x, asList = FALSE, useAssay = "counts",

-        altExpName = "featureSubset") {

+    function(x, asList = FALSE, altExpName = "featureSubset") {

         altExp <- SingleCellExperiment::altExp(x, altExpName)

         logLikelihood <- NULL

@@ -8,12 +8,7 @@

 \usage{

 selectBestModel(x, ...)

-\S4method{selectBestModel}{SingleCellExperiment}(

-  x,

-  asList = FALSE,

-  useAssay = "counts",

-  altExpName = "featureSubset"

-)

+\S4method{selectBestModel}{SingleCellExperiment}(x, asList = FALSE, altExpName = "featureSubset")

 \S4method{selectBestModel}{celdaList}(x, asList = FALSE)

 }

@@ -33,10 +28,6 @@ best model as a

 \code{celdaList} object or not. If \code{FALSE}, return the best model as a

 corresponding celda model object.}

-\item{useAssay}{A string specifying which \code{assay}

-slot to use if \code{x} is a

-\linkS4class{SingleCellExperiment} object. Default "counts".}

-

 \item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot

 to use. Default "featureSubset".}

 }

@@ -9,7 +9,7 @@

 \usage{

 subsetCeldaList(x, ...)

-\S4method{subsetCeldaList}{SingleCellExperiment}(x, params, useAssay = "counts", altExpName = "featureSubset")

+\S4method{subsetCeldaList}{SingleCellExperiment}(x, params, altExpName = "featureSubset")

 \S4method{subsetCeldaList}{celdaList}(x, params)

 }

@@ -27,10 +27,6 @@ subsetCeldaList(x, ...)

 \item{params}{List. List of parameters used to subset the matching celda

 models in list \code{"celda_grid_search"} in \code{metadata(x)}.}

-\item{useAssay}{A string specifying which \code{assay}

-slot to use if \code{x} is a

-\linkS4class{SingleCellExperiment} object. Default "counts".}

-

 \item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot

 to use. Default "featureSubset".}

 }