Merge pull request #309 from zhewa/master

Fix bioc doc warning

DESCRIPTION

@@ -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")),

R/accessors.R

@@ -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

R/celdaGridSearch.R

@@ -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

R/celdaProbabilityMap.R

@@ -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

R/celdaUMAP.R

@@ -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, ...) {

R/celda_C.R

@@ -1,19 +1,19 @@
 #' @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}
 #'  with the matrix located in the 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.
@@ -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

R/celda_CG.R

@@ -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.

R/celda_G.R

@@ -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.