@@ -1,6 +1,6 @@

 Package: celda

 Title: CEllular Latent Dirichlet Allocation

-Version: 1.5.10

+Version: 1.5.11

 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",

     role = c("aut", "cre")),

     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),

@@ -8,10 +8,10 @@

 #'  \item A \linkS4class{SingleCellExperiment} object returned by

 #'  \link{celda_C}, or \link{celda_CG}, with the matrix

 #'  located in the \code{useAssay} assay slot. The

-#'  a \link[SingleCellExperiment]{altExp} slot with name \code{altExpName} will

+#'  a \link{altExp} slot with name \code{altExpName} will

 #'  be used. Rows represent features and columns represent cells.

 #'  \item Celda model object.}

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param value Character vector of cell cluster labels for replacements. Works

 #'  only if \code{x} is a \linkS4class{SingleCellExperiment} object.

@@ -85,7 +85,7 @@ setReplaceMethod("celdaClusters", signature(x = "SingleCellExperiment"),

 #'  \link{celda_G}, or \link{celda_CG}, with the matrix

 #'  located in the \code{useAssay} assay slot.

 #'  Rows represent features and columns represent cells.

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param value Character vector of feature module labels for replacements.

 #'  Works only if \code{x} is a \linkS4class{SingleCellExperiment} object.

@@ -141,7 +141,7 @@ setReplaceMethod("celdaModules", signature(sce = "SingleCellExperiment"),

 #'  located in the \code{useAssay} assay slot.

 #'  Rows represent features and columns represent cells.

 #'  \item A celda model object.}

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param value Character vector of sample labels for replacements. Works

 #'  only is \code{x} is a \linkS4class{SingleCellExperiment} object.

@@ -263,7 +263,7 @@ setMethod("matrixNames",

 #'  priors from the celdaList object when it was created.

 #' @param x An object of class \linkS4class{SingleCellExperiment} or class

 #'  \code{celdaList}.

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

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

 #' @return Data Frame. Contains details on the various K/L parameters, chain

@@ -310,7 +310,7 @@ setMethod("runParams",

 #'  \link{celdaGridSearch} run.

 #' @param x An object of class \linkS4class{SingleCellExperiment} or

 #'  \code{celdaList}.

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

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

 #' @return List. Contains one celdaModel object for each of the parameters

@@ -357,7 +357,7 @@ setMethod("resList",

 #'  \link{celda_C}, \link{celda_G} or \link{celda_CG}.

 #' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object

 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

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

 #' @return Character. The celda model. Can be one of "celda_C", "celda_G", or

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

 #'  with the matrix located in the assay slot under \code{useAssay}.

 #'  Rows represent features and columns represent cells.

 #' @param useAssay A string specifying the name of the

-#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".

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

+#'  \link{assay} slot to use. Default "counts".

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param model Celda model. Options available in \link{availableModels}.

 #' @param paramsTest List. A list denoting the combinations of parameters to

@@ -45,7 +45,7 @@

 #'  and main process. Default "Celda".

 #' @return A \linkS4class{SingleCellExperiment} object. Function

 #'  parameter settings and celda model results are stored in the

-#'  \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot.

+#'  \link{metadata} \code{"celda_grid_search"} slot.

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

 #' @seealso \link{celda_G} for feature clustering, \link{celda_C} for

 #'  clustering of cells, and \link{celda_CG} for simultaneous clustering of

@@ -440,7 +440,7 @@ 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 altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

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

 #' @return One of

@@ -451,10 +451,10 @@ setMethod("celdaGridSearch",

 #'  \code{"celda_grid_search"} slot in \code{metadata(x)} matches

 #'  the given criteria, a new \linkS4class{SingleCellExperiment} object

 #'  with the matching model stored in the

-#'  \link[S4Vectors]{metadata}

+#'  \link{metadata}

 #'  \code{"celda_parameters"} slot will be returned. Otherwise, a new

 #'  \linkS4class{SingleCellExperiment} object with the subset models stored

-#'  in the \link[S4Vectors]{metadata}

+#'  in the \link{metadata}

 #'  \code{"celda_grid_search"} slot will be returned.

 #'  \item A new \code{celdaList} object containing all models matching the

 #'  provided criteria in \code{params}. If only one item in the

@@ -581,7 +581,7 @@ 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 altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

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

 #' @return One of

@@ -591,10 +591,10 @@ setMethod("subsetCeldaList",

 #'  \code{metadata(x)}. If there is only one set of parameters,

 #'  a new \linkS4class{SingleCellExperiment} object

 #'  with the matching model stored in the

-#'  \link[S4Vectors]{metadata}

+#'  \link{metadata}

 #'  \code{"celda_parameters"} slot will be returned. Otherwise, a new

 #'  \linkS4class{SingleCellExperiment} object with the subset models stored

-#'  in the \link[S4Vectors]{metadata}

+#'  in the \link{metadata}

 #'  \code{"celda_grid_search"} slot will be returned.

 #'  \item A new \code{celdaList} object containing one model with the best

 #'  log-likelihood for each set of parameters. If only one set of parameters

@@ -4,9 +4,9 @@

 #'  populations and samples).

 #' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object

 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

 #'  slot to use. Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param level Character. One of "cellPopulation" or "Sample".

 #'  "cellPopulation" will display the absolute probabilities and relative

@@ -8,9 +8,9 @@

 #'  transformed before applying UMAP.

 #' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object

 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

 #'  slot to use. Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param maxCells Integer. Maximum number of cells to plot. Cells will be

 #'  randomly subsampled if \code{ncol(sce) > maxCells}. Larger numbers of cells

@@ -62,7 +62,7 @@

 #' @param ... Additional parameters to pass to \link[uwot]{umap}.

 #' @return \code{sce} with UMAP coordinates

 #'  (columns "celda_UMAP1" & "celda_UMAP2") added to

-#'  \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_UMAP")}.

+#'  \code{\link{reducedDim}(sce, "celda_UMAP")}.

 #' @export

 setGeneric("celdaUmap",

     function(sce, ...) {

@@ -1,10 +1,10 @@

 #' @title Cell clustering with Celda

 #' @description Clusters the columns of a count matrix containing single-cell

 #'  data into K subpopulations. The

-#'  \code{useAssay} \link[SummarizedExperiment]{assay} slot in

-#'  \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if

+#'  \code{useAssay} \link{assay} slot in

+#'  \code{altExpName} \link{altExp} slot will be used if

 #'  it exists. Otherwise, the \code{useAssay}

-#'  \link[SummarizedExperiment]{assay} slot in \code{x} will be used if

+#'  \link{assay} slot in \code{x} will be used if

 #'  \code{x} is a \linkS4class{SingleCellExperiment} object.

 #' @param x A numeric \link{matrix} of counts or a

 #'  \linkS4class{SingleCellExperiment}

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

 #'  \code{altExp(x, altExpName)}.

 #'  Rows represent features and columns represent cells.

 #' @param useAssay A string specifying the name of the

-#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".

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

+#'  \link{assay} slot to use. Default "counts".

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param sampleLabel Vector or factor. Denotes the sample label for each cell

 #'  (column) in the count matrix.

@@ -59,10 +59,10 @@

 #' @param verbose Logical. Whether to print log messages. Default TRUE.

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

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object. Function

-#'  parameter settings are stored in the \link[S4Vectors]{metadata}

+#'  parameter settings are stored in the \link{metadata}

 #'  \code{"celda_parameters"} slot.

 #'  Columns \code{celda_sample_label} and \code{celda_cell_cluster} in

-#'  \link[SummarizedExperiment]{colData} contain sample labels and celda cell

+#'  \link{colData} contain sample labels and celda cell

 #'  population clusters.

 #' @seealso \link{celda_G} for feature clustering and \link{celda_CG} for

 #'  simultaneous clustering of features and cells. \link{celdaGridSearch} can

@@ -1,19 +1,19 @@

 #' @title Cell and feature clustering with Celda

 #' @description Clusters the rows and columns of a count matrix containing

 #'  single-cell data into L modules and K subpopulations, respectively. The

-#'  \code{useAssay} \link[SummarizedExperiment]{assay} slot in

-#'  \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if

+#'  \code{useAssay} \link{assay} slot in

+#'  \code{altExpName} \link{altExp} slot will be used if

 #'  it exists. Otherwise, the \code{useAssay}

-#'  \link[SummarizedExperiment]{assay} slot in \code{x} will be used if

+#'  \link{assay} slot in \code{x} will be used if

 #'  \code{x} is a \linkS4class{SingleCellExperiment} object.

 #' @param x A numeric \link{matrix} of counts or a

 #'  \linkS4class{SingleCellExperiment}

-#'  with the matrix located in the \link[SummarizedExperiment]{assay}

+#'  with the matrix located in the \link{assay}

 #'  slot under \code{useAssay} in \code{altExp(x, altExpName)}.

 #'  Rows represent features and columns represent cells.

 #' @param useAssay A string specifying the name of the

-#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".

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

+#'  \link{assay} slot to use. Default "counts".

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param sampleLabel Vector or factor. Denotes the sample label for each cell

 #'  (column) in the count matrix.

@@ -35,11 +35,12 @@

 #'  likelihood to stop inference. Default 10.

 #' @param maxIter Integer. Maximum number of iterations of Gibbs sampling to

 #'  perform. Default 200.

-#' @param splitOnIter Integer. On every `splitOnIter` iteration, a heuristic

+#' @param splitOnIter Integer. On every \code{splitOnIter} iteration,

+#'  a heuristic

 #'  will be applied to determine if a cell population or feature module should

 #'  be reassigned and another cell population or feature module should be split

 #'  into two clusters. To disable splitting, set to -1. Default 10.

-#' @param splitOnLast Integer. After `stopIter` iterations have been

+#' @param splitOnLast Integer. After \code{stopIter} iterations have been

 #'  performed without improvement, a heuristic will be applied to determine if

 #'  a cell population or feature module should be reassigned and another cell

 #'  population or feature module should be split into two clusters. If a split

@@ -52,32 +53,32 @@

 #'  With 'random', cells are randomly assigned to a populations. With 'split',

 #'  cells will be split into sqrt(K) populations and then each popluation will

 #'  be subsequently split into another sqrt(K) populations. With 'predefined',

-#'  values in `zInit` will be used to initialize `z`. Default 'split'.

+#'  values in \code{zInit} will be used to initialize \code{z}. Default 'split'.

 #' @param yInitialize Chararacter. One of 'random', 'split', or 'predefined'.

 #'  With 'random', features are randomly assigned to a modules. With 'split',

 #'  features will be split into sqrt(L) modules and then each module will be

 #'  subsequently split into another sqrt(L) modules. With 'predefined', values

-#'  in `yInit` will be used to initialize `y`. Default 'split'.

+#'  in \code{yInit} will be used to initialize \code{y}. Default 'split'.

 #' @param zInit Integer vector. Sets initial starting values of z. If NULL,

 #'  starting values for each cell will be randomly sampled from 1:K. 'zInit'

-#'  can only be used when `initialize' = 'random'`. Default NULL.

+#'  can only be used when \code{initialize = "random"}. Default NULL.

 #' @param yInit Integer vector. Sets initial starting values of y. If NULL,

 #'  starting values for each feature will be randomly sampled from 1:L.

-#'  'yInit' can only be used when `initialize = 'random'`. Default NULL.

-#' @param countChecksum Character. An MD5 checksum for the `counts` matrix.

+#'  'yInit' can only be used when \code{initialize = "random"}. Default NULL.

+#' @param countChecksum Character. An MD5 checksum for the counts matrix.

 #'  Default NULL.

 #' @param logfile Character. Messages will be redirected to a file named

 #'  `logfile`. If NULL, messages will be printed to stdout.  Default NULL.

 #' @param verbose Logical. Whether to print log messages. Default TRUE.

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

 #' @return A \linkS4class{SingleCellExperiment} object. Function

-#'  parameter settings are stored in \link[S4Vectors]{metadata}

-#'  \code{"celda_parameters"} in \link[SingleCellExperiment]{altExp} slot.

-#'  In \link[SingleCellExperiment]{altExp} slot,

+#'  parameter settings are stored in \link{metadata}

+#'  \code{"celda_parameters"} in \link{altExp} slot.

+#'  In \link{altExp} slot,

 #'  columns \code{celda_sample_label} and \code{celda_cell_cluster} in

-#'  \link[SummarizedExperiment]{colData} contain sample labels and celda cell

+#'  \link{colData} contain sample labels and celda cell

 #'  population clusters. Column \code{celda_feature_module} in

-#'  \link[SummarizedExperiment]{rowData} contains feature modules.

+#'  \link{rowData} contains feature modules.

 #' @seealso \link{celda_G} for feature clustering and \link{celda_C} for

 #'  clustering cells. \link{celdaGridSearch} can be used to run multiple

 #'  values of K/L and multiple chains in parallel.

@@ -1,18 +1,18 @@

 #' @title Feature clustering with Celda

 #' @description Clusters the rows of a count matrix containing single-cell data

 #'  into L modules. The

-#'  \code{useAssay} \link[SummarizedExperiment]{assay} slot in

-#'  \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if

+#'  \code{useAssay} \link{assay} slot in

+#'  \code{altExpName} \link{altExp} slot will be used if

 #'  it exists. Otherwise, the \code{useAssay}

-#'  \link[SummarizedExperiment]{assay} slot in \code{x} will be used if

+#'  \link{assay} slot in \code{x} will be used if

 #'  \code{x} is a \linkS4class{SingleCellExperiment} object.

 #' @param x A numeric \link{matrix} of counts or a

 #'  \linkS4class{SingleCellExperiment}

 #'  with the matrix located in the assay slot under \code{useAssay}.

 #'  Rows represent features and columns represent cells.

 #' @param useAssay A string specifying the name of the

-#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".

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

+#'  \link{assay} slot to use. Default "counts".

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param L Integer. Number of feature modules.

 #' @param beta Numeric. Concentration parameter for Phi. Adds a pseudocount to

@@ -53,9 +53,9 @@

 #' @param verbose Logical. Whether to print log messages. Default TRUE.

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

 #' @return A \linkS4class{SingleCellExperiment} object. Function

-#'  parameter settings are stored in the \link[S4Vectors]{metadata}

+#'  parameter settings are stored in the \link{metadata}

 #'  \code{"celda_parameters"} slot. Column \code{celda_feature_module} in

-#'  \link[SummarizedExperiment]{rowData} contains feature modules.

+#'  \link{rowData} contains feature modules.

 #' @seealso \link{celda_C} for cell clustering and \link{celda_CG} for

 #'  simultaneous clustering of features and cells. \link{celdaGridSearch} can

 #'  be used to run multiple values of L and multiple chains in parallel.

@@ -137,7 +137,7 @@ normalizeCounts <- function(counts,

 #' @param sce \linkS4class{SingleCellExperiment} object returned from

 #'  \link{celda_C} or \link{celda_CG}. Must contain column

 #'  \code{celda_cell_cluster} in

-#'  \code{\link[SummarizedExperiment]{colData}(altExp(sce, altExpName))}.

+#'  \code{\link{colData}(altExp(sce, altExpName))}.

 #' @param from Numeric vector. Unique values in the range of

 #'  \code{seq(celdaClusters(sce, altExpName = altExpName))} that correspond to

 #'  the original cluster

@@ -145,7 +145,7 @@ normalizeCounts <- function(counts,

 #' @param to Numeric vector. Unique values in the range of

 #'  \code{seq(celdaClusters(sce, altExpName = altExpName))} that correspond to

 #'  the new cluster labels.

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @return \linkS4class{SingleCellExperiment} object with recoded cell

 #'  cluster labels.

@@ -188,13 +188,13 @@ recodeClusterZ <- function(sce, from, to, altExpName = "featureSubset") {

 #' @param sce \linkS4class{SingleCellExperiment} object returned from

 #'  \link{celda_G} or \link{celda_CG}. Must contain column

 #'  \code{celda_feature_module} in

-#'  \code{\link[SummarizedExperiment]{rowData}(altExp(sce, altExpName))}.

+#'  \code{\link{rowData}(altExp(sce, altExpName))}.

 #' @param from Numeric vector. Unique values in the range of

 #'  \code{seq(celdaModules(sce))} that correspond to the original module labels

 #'  in \code{sce}.

 #' @param to Numeric vector. Unique values in the range of

 #'  \code{seq(celdaModules(sce))} that correspond to the new module labels.

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @return @return \linkS4class{SingleCellExperiment} object with recoded

 #'  feature module labels.

@@ -525,9 +525,9 @@ distinctColors <- function(n,

 #'  \link{celda_G}, or \link{celda_CG}, with the matrix

 #'  located in the \code{useAssay} assay slot.

 #'  Rows represent features and columns represent cells.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

 #'  slot to use. Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param outputFile File name for feature module table. If NULL, file will

 #'  not be created. Default NULL.

@@ -3,9 +3,9 @@

 #'  clustering results.

 #' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object

 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

 #'  slot to use. Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param featureIx Integer vector. Select features for display in heatmap. If

 #'  NULL, no subsetting will be performed. Default NULL. \strong{Only used for

@@ -8,9 +8,9 @@

 #'  Module probabilities are square-root transformed before applying tSNE.

 #' @param sce A \linkS4class{SingleCellExperiment} object

 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

 #'  slot to use. Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param maxCells Integer. Maximum number of cells to plot. Cells will be

 #'  randomly subsampled if \code{ncol(counts) > maxCells}. Larger numbers of

@@ -48,7 +48,7 @@

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

 #' @return \code{sce} with t-SNE coordinates

 #'  (columns "celda_tSNE1" & "celda_tSNE2") added to

-#'  \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_tSNE")}.

+#'  \code{\link{reducedDim}(sce, "celda_tSNE")}.

 #' @export

 setGeneric("celdaTsne",

     function(sce, ...) {

@@ -11,17 +11,17 @@

 #'  \code{celdaModel}. Dimensions and MD5 checksum will be checked by

 #'  \link{compareCountMatrix}.

 #' @param useAssay A string specifying the name of the

-#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".

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

+#'  \link{assay} slot to use. Default "counts".

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

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

 #' @return A \linkS4class{SingleCellExperiment} object. Function

-#'  parameter settings are stored in the \link[S4Vectors]{metadata}

+#'  parameter settings are stored in the \link{metadata}

 #'  \code{"celda_parameters"} slot.

 #'  Columns \code{celda_sample_label} and \code{celda_cell_cluster} in

-#'  \link[SummarizedExperiment]{colData} contain sample labels and celda cell

+#'  \link{colData} contain sample labels and celda cell

 #'  population clusters. Column \code{celda_feature_module} in

-#'  \link[SummarizedExperiment]{rowData} contain feature modules.

+#'  \link{rowData} contain feature modules.

 #' @export

 setGeneric("celdatosce", function(celdaModel, counts, ...) {

     standardGeneric("celdatosce")})

@@ -8,9 +8,9 @@

 #'  \link{celda_C}, \link{celda_G}, or \link{celda_CG}, with the matrix

 #'  located in the \code{useAssay} assay slot.

 #'  Rows represent features and columns represent cells.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

 #'  slot to use. Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param log Logical. If \code{FALSE}, then the normalized conditional

 #'  probabilities will be returned. If \code{TRUE}, then the unnormalized log

@@ -7,10 +7,10 @@

 #'  Rows represent features and columns represent cells. Must contain cluster

 #'  labels in \code{celdaClusters(x, altExpName = altExpName)} if \code{x} is a

 #'  \linkS4class{SingleCellExperiment} object.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

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

 #'  \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param celdaMod Celda object of class `celda_C` or `celda_CG`.

 #' @param c1 Integer vector. Cell populations to include in group 1 for the

@@ -11,10 +11,10 @@

 #'  \item Integer counts matrix. Rows represent features and columns represent

 #'  cells. This matrix should be the same as the one used to generate

 #'  \code{celdaMod}.}

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

 #'  slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object.

 #'  Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param celdaMod Celda model object. Only works if \code{x} is an integer

 #'  counts matrix.

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

 #'  Rows represent features and columns represent cells.

 #' @param feature Character vector. Identify feature modules for the specified

 #'  feature names. \code{feature} must match the rownames of \code{sce}.

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param exactMatch Logical. Whether to look for exactMatch of the gene name

 #'  within counts matrix. Default \code{TRUE}.

@@ -9,10 +9,10 @@

 #'  \linkS4class{SingleCellExperiment}

 #'  with the matrix located in the assay slot under \code{useAssay}.

 #'  Rows represent features and columns represent cells.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

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

 #'  \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param class Vector of cell cluster labels.

 #' @param oneoffMetric A character string. What one-off metric to run, either

@@ -9,10 +9,10 @@

 #'  with the matrix located in the assay slot under \code{useAssay}.

 #'  Rows represent features and columns represent cells. Rownames of the

 #'  matrix or \linkS4class{SingleCellExperiment} object should be gene names.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

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

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

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param celdaModel Celda object of class \code{celda_G} or \code{celda_CG}.

 #' @param databases Character vector. Name of reference database. Available

@@ -5,9 +5,9 @@

 #'  \link{celda_C}, \link{celda_G}, or \link{celda_CG}, with the matrix

 #'  located in the \code{useAssay} assay slot.

 #'  Rows represent features and columns represent cells.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

 #'  slot to use. Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param celdaMod celda model object. Ignored if \code{x} is a

 #'  \linkS4class{SingleCellExperiment} object.

@@ -154,7 +154,7 @@ setMethod("logLikelihood", signature(x = "matrix", celdaMod = "celda_CG"),

 #' @param x A \linkS4class{SingleCellExperiment} object

 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}, or a celda

 #'  model object.

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

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

 #' @return Numeric. The log-likelihood at each step of Gibbs sampling used to

@@ -205,7 +205,7 @@ setMethod("logLikelihoodHistory",

 #' @param x A \linkS4class{SingleCellExperiment} object

 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}, or a celda

 #'  model object.

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

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

 #' @export

@@ -10,10 +10,10 @@

 #'  \linkS4class{SingleCellExperiment}

 #'  with the matrix located in the assay slot under \code{useAssay}.

 #'  Rows represent features and columns represent cells.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

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

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

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param featureModule Integer Vector. The featureModule(s) to display.

 #'  Multiple modules can be included in a vector. Default \code{NULL} which

@@ -10,10 +10,10 @@

 #'  \item Integer counts matrix. Rows represent features and columns represent

 #'  cells. This matrix should be the same as the one used to generate

 #'  \code{celdaMod}.}

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

 #'  slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object.

 #'  Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param celdaMod Celda model object. Only works if \code{x} is an integer

 #'  counts matrix.

@@ -347,10 +347,10 @@ setMethod(

 #'  Rows represent features and columns represent cells. Must contain

 #'  "celda_grid_search" slot in \code{metadata(x)} if \code{x} is a

 #'  \linkS4class{SingleCellExperiment} object.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

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

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

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param celdaList Object of class 'celdaList'. Used only if \code{x} is a

 #'  matrix object.

@@ -483,7 +483,7 @@ setMethod("resamplePerplexity",

 #'  or \code{recursiveSplitCell}. Must contain a list named

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

 #'  \item celdaList object.}

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param sep Numeric. Breaks in the x axis of the resulting plot.

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

@@ -743,7 +743,7 @@ setMethod("plotGridSearchPerplexity",

 #'  or \code{recursiveSplitCell}. Must contain a list named

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

 #'  \item celdaList object.}

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param sep Numeric. Breaks in the x axis of the resulting plot.

 #' @param n Integer. Width of the rolling window. Default 10.

@@ -12,15 +12,15 @@

 #'  reduction output.

 #' @param dim2 Numeric vector. Second dimension from data dimension

 #'  reduction output.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

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

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

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param size Numeric. Sets size of point on plot. Default 1.

 #' @param xlab Character vector. Label for the x-axis. Default 'Dimension_1'.

 #' @param ylab Character vector. Label for the y-axis. Default 'Dimension_2'.

-#' @param limits Passed to \link[ggplot2]{scale_colour_gradient2}. The range

+#' @param limits Passed to \link{scale_colour_gradient2}. The range

 #'  of color scale.

 #' @param colorLow Character. A color available from `colors()`.

 #'  The color will be used to signify the lowest values on the scale.

@@ -291,10 +291,10 @@ setMethod("plotDimReduceGrid",

 #'  dimension reduction output.

 #' @param dim2 Numeric vector. Second dimension from data dimension

 #'  reduction output.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

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

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

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param features Character vector. Features in the rownames of counts to plot.

 #' @param headers Character vector. If `NULL`, the corresponding rownames are

@@ -309,7 +309,7 @@ setMethod("plotDimReduceGrid",

 #' @param trim Numeric vector. Vector of length two that specifies the lower

 #'  and upper bounds for the data. This threshold is applied after row scaling.

 #'  Set to NULL to disable. Default \code{c(-1,1)}.

-#' @param limits Passed to \link[ggplot2]{scale_colour_gradient2}. The range

+#' @param limits Passed to \link{scale_colour_gradient2}. The range

 #'  of color scale.

 #' @param size Numeric. Sets size of point on plot. Default 1.

 #' @param xlab Character vector. Label for the x-axis. Default "Dimension_1".

@@ -576,10 +576,10 @@ setMethod("plotDimReduceFeature",

 #'  First dimension from data dimension reduction output.

 #' @param dim2 Numeric vector.

 #'  Second dimension from data dimension reduction output.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

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

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

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param celdaMod Celda object of class "celda_G" or "celda_CG". Used only if

 #'  \code{x} is a matrix object.

@@ -587,7 +587,7 @@ setMethod("plotDimReduceFeature",

 #'  e.g. c("1", "2").

 #' @param rescale Logical.

 #'  Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE.

-#' @param limits Passed to \link[ggplot2]{scale_colour_gradient}. The range

+#' @param limits Passed to \link{scale_colour_gradient}. The range

 #'  of color scale.

 #' @param size Numeric. Sets size of point on plot. Default 1.

 #' @param xlab Character vector. Label for the x-axis. Default "Dimension_1".

@@ -814,7 +814,7 @@ setMethod("plotDimReduceModule",

 #'  \code{reducedDimNames(x)} if \code{x} is a

 #'  \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and

 #'  \code{dim2} are set.

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param dim1 Numeric vector. First dimension from data

 #'  dimension reduction output.

@@ -1027,10 +1027,10 @@ setMethod("plotDimReduceCluster",

 #'  with the matrix located in the assay slot under \code{useAssay}. Rows

 #'  represent features and columns represent cells.

 #' @param features Character vector. Uses these genes for plotting.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

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

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

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param celdaMod Celda object of class "celda_G" or "celda_CG". Used only if

 #'  \code{x} is a matrix object.

@@ -90,9 +90,9 @@

 #'  with the matrix located in the assay slot under \code{useAssay}.

 #'  Rows represent features and columns represent cells.

 #' @param useAssay A string specifying the name of the

-#'  \link[SummarizedExperiment]{assay}

+#'  \link{assay}

 #'  slot to use. Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param sampleLabel Vector or factor. Denotes the sample label for each cell

 #'  (column) in the count matrix.

@@ -137,7 +137,7 @@

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

 #' @return A \linkS4class{SingleCellExperiment} object. Function

 #'  parameter settings and celda model results are stored in the

-#'  \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. The models in

+#'  \link{metadata} \code{"celda_grid_search"} slot. The models in

 #'  the list will be of class \code{celda_C} if \code{yInit = NULL} or

 #'  \code{celda_CG} if \code{zInit} is set.

 #' @seealso \link{recursiveSplitModule} for recursive splitting of feature

@@ -859,10 +859,10 @@ setMethod("recursiveSplitCell",

 #'  \linkS4class{SingleCellExperiment}

 #'  with the matrix located in the assay slot under \code{useAssay}.

 #'  Rows represent features and columns represent cells.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

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

 #'  \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param initialL Integer. Minimum number of modules to try.

 #' @param maxL Integer. Maximum number of modules to try.

@@ -905,7 +905,7 @@ setMethod("recursiveSplitCell",

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

 #' @return A \linkS4class{SingleCellExperiment} object. Function

 #'  parameter settings and celda model results are stored in the

-#'  \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. The models in

+#'  \link{metadata} \code{"celda_grid_search"} slot. The models in

 #'  the list will be of class \link{celda_G} if \code{zInit = NULL} or

 #'  \link{celda_CG} if \code{zInit} is set.

 #' @seealso \code{recursiveSplitCell} for recursive splitting of cell

@@ -3,8 +3,8 @@

 #'  Select features with at least \code{minCount} counts

 #'  in at least \code{minCell} cells. A \linkS4class{SingleCellExperiment}

 #'  object with subset features will be stored in the

-#'  \link[SingleCellExperiment]{altExp} slot with name \code{altExpName}.

-#'  The name of the \code{assay} slot in \link[SingleCellExperiment]{altExp}

+#'  \link{altExp} slot with name \code{altExpName}.

+#'  The name of the \code{assay} slot in \link{altExp}

 #'  will be the same as \code{useAssay}.

 #' @param x A numeric \link{matrix} of counts or a

 #'  \linkS4class{SingleCellExperiment}

@@ -13,13 +13,13 @@

 #' @param minCount Minimum number of counts required for feature selection.

 #' @param minCell Minimum number of cells required for feature selection.

 #' @param useAssay A string specifying the name of the

-#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".

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

+#'  \link{assay} slot to use. Default "counts".

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

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

 #' @return A \linkS4class{SingleCellExperiment} object with a

-#'  \code{altExpName} \link[SingleCellExperiment]{altExp} slot. Function

-#'  parameter settings are stored in the \link[S4Vectors]{metadata}

+#'  \code{altExpName} \link{altExp} slot. Function

+#'  parameter settings are stored in the \link{metadata}

 #'  \code{"select_features"} slot.

 #' @export

 setGeneric("selectFeatures", function(x, ...) {

@@ -41,13 +41,13 @@

 #'  \link[withr]{with_seed} are made.

 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with

 #'  simulated count matrix stored in the "counts" assay slot. Function

-#'  parameter settings are stored in the \link[S4Vectors]{metadata} slot. For

+#'  parameter settings are stored in the \link{metadata} slot. For

 #'  \code{"celda_CG"} and \code{"celda_C"} models,

 #'  columns \code{celda_sample_label} and \code{celda_cell_cluster} in

-#'  \link[SummarizedExperiment]{colData} contain simulated sample labels and

+#'  \link{colData} contain simulated sample labels and

 #'  cell population clusters. For \code{"celda_CG"} and \code{"celda_G"}

 #'  models, column \code{celda_feature_module} in

-#'  \link[SummarizedExperiment]{rowData} contains simulated gene modules.

+#'  \link{rowData} contains simulated gene modules.

 #' @examples

 #' sce <- simulateCells()

 #' @export

@@ -5,9 +5,9 @@

 #' @param x A \linkS4class{SingleCellExperiment} object

 #'  with the matrix located in the assay slot under \code{useAssay}.

 #'  Rows represent features and columns represent cells.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

 #'  slot to use for \code{x}. Default "counts".

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

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param module Integer. The module to be split.

 #' @param n Integer. How many modules should \code{module} be split into.

@@ -18,7 +18,7 @@

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

 #' @return A updated \linkS4class{SingleCellExperiment} object with new

 #'  feature modules stored in column \code{celda_feature_module} in

-#'  \code{\link[SummarizedExperiment]{rowData}(x)}.

+#'  \code{\link{rowData}(x)}.

 #' @export

 setGeneric("splitModule",

     function(x, ...) {

@@ -19,7 +19,7 @@ model object.}

 \item{...}{Ignored. Placeholder to prevent check warning.}

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

+\item{altExpName}{The name for the \link{altExp} slot

 to use. Default "featureSubset".}

 }

 \value{

@@ -26,13 +26,13 @@ celdaClusters(x, altExpName = "featureSubset") <- value

 \item A \linkS4class{SingleCellExperiment} object returned by

 \link{celda_C}, or \link{celda_CG}, with the matrix

 located in the \code{useAssay} assay slot. The

-a \link[SingleCellExperiment]{altExp} slot with name \code{altExpName} will

+a \link{altExp} slot with name \code{altExpName} will

 be used. Rows represent features and columns represent cells.

 \item Celda model object.}}

 \item{...}{Ignored. Placeholder to prevent check warning.}

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

+\item{altExpName}{The name for the \link{altExp} slot

 to use. Default "featureSubset".}

 \item{value}{Character vector of cell cluster labels for replacements. Works

@@ -51,9 +51,9 @@ Rows represent features and columns represent cells.}

 \item{...}{Ignored. Placeholder to prevent check warning.}

 \item{useAssay}{A string specifying the name of the

-\link[SummarizedExperiment]{assay} slot to use. Default "counts".}

+\link{assay} slot to use. Default "counts".}

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

+\item{altExpName}{The name for the \link{altExp} slot

 to use. Default "featureSubset".}

 \item{model}{Celda model. Options available in \link{availableModels}.}

@@ -98,7 +98,7 @@ and main process. Default "Celda".}

 \value{

 A \linkS4class{SingleCellExperiment} object. Function

  parameter settings and celda model results are stored in the

- \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot.

+ \link{metadata} \code{"celda_grid_search"} slot.

 }

 \description{

 Run Celda with different combinations of parameters and

@@ -22,10 +22,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.}

 \item{...}{Additional parameters passed to \link{plotHeatmap}.}

-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}

+\item{useAssay}{A string specifying which \link{assay}

 slot to use. Default "counts".}

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

+\item{altExpName}{The name for the \link{altExp} slot

 to use. Default "featureSubset".}

 \item{featureIx}{Integer vector. Select features for display in heatmap. If

@@ -16,7 +16,7 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.}

 \item{...}{Ignored. Placeholder to prevent check warning.}

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