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Edit links to documentation

unknown authored on 22/10/2020 03:39:09
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@@ -52,7 +52,7 @@
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 #'
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 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with
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 #'  'decontX_Contamination' and 'decontX_Clusters' added to the
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-#'  \link[SummarizedExperiment]{colData} slot. Additionally, the
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+#'  \link{colData} slot. Additionally, the
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 #' decontaminated counts will be added as an assay called 'decontXCounts'.
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 #' @examples
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 #' data(scExample, package = "singleCellTK")
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@@ -46,7 +46,7 @@
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 #' @param df See \link[DropletUtils]{emptyDrops} for more information. Default \code{20}.
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 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with the
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 #'  \link[DropletUtils]{barcodeRanks} output table appended to the
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-#'  \link[SummarizedExperiment]{colData} slot. The columns include
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+#'  \link{colData} slot. The columns include
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 #'  \emph{dropletUtils_BarcodeRank_Knee} and \emph{dropletUtils_BarcodeRank_Knee}
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 #'  Please refer to the documentation of \link[DropletUtils]{barcodeRanks} for
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 #'  details.
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@@ -45,7 +45,7 @@
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 #' @param BPPARAM See \link[DropletUtils]{emptyDrops} for more information.
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 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with the
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 #'  \link[DropletUtils]{emptyDrops} output table appended to the
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-#'  \link[SummarizedExperiment]{colData} slot. The columns include
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+#'  \link{colData} slot. The columns include
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 #'  \emph{emptyDrops_total}, \emph{emptyDrops_logprob},
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 #'  \emph{emptyDrops_pvalue}, \emph{emptyDrops_limited}, \emph{emptyDrops_fdr}.
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 #'  Please refer to the documentation of \link[DropletUtils]{emptyDrops} for
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@@ -6,20 +6,20 @@
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 #' @param inSCE A \code{\link[SingleCellExperiment]{SingleCellExperiment}}
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 #' object.
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 #' @param useAssay A single \code{character}, specifying which
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-#' \code{\link[SummarizedExperiment]{assay}} to perform the clustering algorithm
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+#' \code{\link{assay}} to perform the clustering algorithm
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 #' on. Default \code{NULL}.
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 #' @param useReducedDim A single \code{character}, specifying which
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-#' low-dimension representation (\code{\link[SingleCellExperiment]{reducedDim}})
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+#' low-dimension representation (\code{\link{reducedDim}})
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 #' to perform the clustering algorithm on. Default \code{NULL}.
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 #' @param useAltExp A single \code{character}, specifying the assay which
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-#' \code{\link[SingleCellExperiment]{altExp}} to perform the clustering
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+#' \code{\link{altExp}} to perform the clustering
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 #' algorithm on. Default \code{NULL}.
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 #' @param altExpAssay A single \code{character}, specifying which
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-#' \code{\link[SummarizedExperiment]{assay}} in the chosen
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-#' \code{\link[SingleCellExperiment]{altExp}} to work on. Only used when
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+#' \code{\link{assay}} in the chosen
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+#' \code{\link{altExp}} to work on. Only used when
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 #' \code{useAltExp} is set. Default \code{"counts"}.
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 #' @param clusterName A single \code{character}, specifying the name to store
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-#' the cluster label in \code{\link[SummarizedExperiment]{colData}}. Default
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+#' the cluster label in \code{\link{colData}}. Default
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 #' \code{"scranSNN_cluster"}.
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 #' @param k An \code{integer}, the number of nearest neighbors used to construct
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 #' the graph. Smaller value indicates higher resolution and larger number of
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@@ -109,7 +109,7 @@ runScranSNN <- function(inSCE, useAssay = NULL, useReducedDim = NULL,
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 #' low-dimension representation to perform the clustering algorithm on. Default
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 #' \code{"PCA"}.
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 #' @param clusterName A single \code{character}, specifying the name to store
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-#' the cluster label in \code{\link[SummarizedExperiment]{colData}}. Default
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+#' the cluster label in \code{\link{colData}}. Default
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 #' \code{"scranSNN_cluster"}.
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 #' @param nCenters An \code{integer}, the number of centroids (clusters).
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 #' @param nIter An \code{integer}, the maximum number of iterations allowed.
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@@ -9,11 +9,11 @@
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 #' selected.variable features. Default \code{NULL}.
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 #' @param sample Character vector. Indicates which sample each cell belongs to.
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 #' If given a single character, will take the annotation from
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-#' \code{\link[SummarizedExperiment]{colData}}. Default \code{NULL}.
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+#' \code{\link{colData}}. Default \code{NULL}.
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 #' @param reducedDimName A name to store the results of the dimension reduction
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 #' coordinates obtained from this method. Default \code{"UMAP"}.
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 #' @param logNorm Whether the counts will need to be log-normalized prior to
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-#' generating the UMAP via \code{\link[scater]{logNormCounts}}. Default
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+#' generating the UMAP via \code{\link{logNormCounts}}. Default
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 #' \code{TRUE}.
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 #' @param nNeighbors The size of local neighborhood used for manifold
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 #' approximation. Larger values result in more global views of the manifold,
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@@ -29,7 +29,7 @@
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 #' result on a more even dispersal of points. Default \code{0.01}. See
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 #' `?uwot::umap` for more information.
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 #' @param spread The effective scale of embedded points. In combination with
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-#' ‘min_dist’, this determines how clustered/clumped the embedded points are.
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+#' minDist, this determines how clustered/clumped the embedded points are.
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 #' Default \code{1}. See `?uwot::umap` for more information.
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 #' @param pca Logical. Whether to perform dimension reduction with PCA before
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 #' UMAP. Default \code{TRUE}
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@@ -83,7 +83,7 @@
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 #'   with the sample name appended to each colname in colData
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 #' }
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'  \link[DelayedArray]{DelayedArray} object. Default \code{TRUE}.
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+#'  \link{DelayedArray} object. Default \code{TRUE}.
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 #' @details
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 #' \code{importAnnData} converts scRNA-seq data in the AnnData format to the
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 #' \code{SingleCellExperiment} object. The .X slot in AnnData is transposed to the features x cells
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@@ -99,10 +99,10 @@
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 #'  \code{samples}.
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 #' @param class Character. The class of the expression matrix stored in the SCE
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 #'  object. Can be one of "Matrix" (as returned by
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-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by
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+#'  \link{readMM} function), or "matrix" (as returned by
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 #'  \link[base]{matrix} function). Default "Matrix".
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.
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+#'  \link[DelayedArray]{DelayedArray-class} object or not. Default \code{TRUE}.
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 #' @return A \code{SingleCellExperiment} object containing the count
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 #'  matrix, the gene annotation, and the cell annotation.
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 #' @examples
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@@ -433,7 +433,7 @@
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 #' \itemize{
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 #'   \item \code{NULL}. All samples within \code{cellRangerDirs} will be
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 #'    imported. The order of samples will be first determined by the order of
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-#'    \code{cellRangerDirs} and then by \link[base]{list.dirs}. This is only
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+#'    \code{cellRangerDirs} and then by \link{list.dirs}. This is only
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 #'    for the case where \code{cellRangerDirs} is specified.
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 #'   \item A list of vectors containing the folder names for samples to import.
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 #'    Each vector in
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@@ -509,10 +509,10 @@
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 #'  \code{unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE))}.
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 #' @param class Character. The class of the expression matrix stored in the SCE
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 #'  object. Can be one of "Matrix" (as returned by
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-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by
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+#'  \link{readMM} function), or "matrix" (as returned by
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 #'  \link[base]{matrix} function). Default \code{"Matrix"}.
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.
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+#'  \link{DelayedArray} object or not. Default \code{TRUE}.
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 #' @param reference Character vector. The reference genome names. 
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 #'  Default \code{NULL}. If not \code{NULL}, it must gave the length and order as 
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 #'  \code{length(unlist(sampleDirs))} if \code{sampleDirs} is not \code{NULL}.
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@@ -653,10 +653,10 @@ importCellRangerV2 <- function(
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 #'  Default "sample".
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 #' @param class Character. The class of the expression matrix stored in the SCE
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 #'  object. Can be one of "Matrix" (as returned by
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-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by
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+#'  \link{readMM} function), or "matrix" (as returned by
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 #'  \link[base]{matrix} function). Default "Matrix".
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.
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+#'  \link{DelayedArray} object or not. Default \code{TRUE}.
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 #' @return A \code{SingleCellExperiment} object containing the count
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 #'  matrix, the feature annotations, and the cell annotation for the sample.
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 #' @examples
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@@ -737,10 +737,10 @@ importCellRangerV3 <- function(
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 #'  Default "sample".
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 #' @param class Character. The class of the expression matrix stored in the SCE
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 #'  object. Can be one of "Matrix" (as returned by
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-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by
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+#'  \link{readMM} function), or "matrix" (as returned by
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 #'  \link[base]{matrix} function). Default "Matrix".
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.
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+#'  \link{DelayedArray} object or not. Default \code{TRUE}.
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 #' @return A \code{SingleCellExperiment} object containing the count
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 #'  matrix, the feature annotations, and the cell annotation for the sample.
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 #' @examples
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@@ -91,7 +91,7 @@
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 #' @param dataType can be "filtered" or "raw". Default \code{"filtered"}.
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 #' @param rdsFileName File name prefix of the DropEst RDS output. default is "cell.counts"
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.
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+#'  \link{DelayedArray} object or not. Default \code{TRUE}.
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 #' @details
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 #' \code{importDropEst} expects either raw counts matrix stored as "cm_raw" or filtered
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 #' counts matrix stored as "cm" in the DropEst rds output.
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@@ -2,7 +2,7 @@
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 #' @title Retrieve example datasets
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 #' @description Retrieves published example datasets stored in
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 #' \link[SingleCellExperiment]{SingleCellExperiment} using the
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-#' \link[scRNAseq]{scRNAseq} and
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+#' \link{scRNAseq} and
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 #' \link[TENxPBMCData]{TENxPBMCData} packages. See 'Details' for a
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 #' list of available datasets.
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 #' @param dataset Character. Name of the dataset to retrieve.
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@@ -12,16 +12,16 @@
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 #'   \code{"matrix"} will store the data in a standard matrix. Default
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 #'   \code{"Matrix"}.
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'   \link[DelayedArray]{DelayedArray} object or not. Default \code{FALSE}.
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+#'   \link{DelayedArray} object or not. Default \code{FALSE}.
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 #' @details See the list below for the available datasets and their
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 #' descriptions.
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 #' \describe{
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 #' \item{"fluidigm_pollen"}{Retrieved with
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-#' \code{\link[scRNAseq]{ReprocessedFluidigmData}}. Returns a dataset of 65
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+#' \code{\link{ReprocessedFluidigmData}}. Returns a dataset of 65
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 #'  human neural cells from Pollen et al. (2014), each sequenced at high and low
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 #'  coverage (SRA accession SRP041736).}
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 #' \item{"allen_tasic"}{Retrieved with
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-#' \code{\link[scRNAseq]{ReprocessedAllenData}}. Returns a dataset of 379 mouse
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+#' \code{\link{ReprocessedAllenData}}. Returns a dataset of 379 mouse
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 #' brain cells from Tasic et al. (2016).}
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 #' \item{"pbmc3k"}{Retrieved with \code{\link[TENxPBMCData]{TENxPBMCData}}.
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 #'  2,700 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.}
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@@ -31,7 +31,7 @@
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 #' frames instead of file paths. The default is FALSE.
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 #' @param class Character. The class of the expression matrix stored in the SCE
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 #'  object. Can be one of "Matrix" (as returned by
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-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by
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+#'  \link{readMM} function), or "matrix" (as returned by
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 #'  \link[base]{matrix} function). Default "Matrix".
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 #' @param annotFileHeader Whether there's a header (colnames) in the cell annotation file. Default is FALSE  
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 #' @param annotFileRowName Which column is used as the rownames for the cell annotation file. Default is 1 (first column). 
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@@ -41,7 +41,7 @@
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 #' @param featureSep Separater used for the feature annotation file. Default is "\\t".
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 #' @param gzipped Whether the input file is gzipped. Default is "auto" and it will automatically detect whether the file is gzipped. Other options is TRUE or FALSE. 
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.
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+#'  \link{DelayedArray} object or not. Default \code{TRUE}.
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 #' @return a SingleCellExperiment object
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 #' @export
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@@ -4,7 +4,7 @@
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 #' \linkS4class{SingleCellExperiment} object. These gene sets can be used in
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 #' downstream quality control and analysis functions in \link{singleCellTK}.
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 #' @param inSCE Input \linkS4class{SingleCellExperiment} object.
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-#' @param file Character. Path to GMT file. See \link[GSEABase]{getGmt} for
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+#' @param file Character. Path to GMT file. See \link{getGmt} for
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 #' more information on reading GMT files.
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 #' @param collectionName Character. Name of collection to add gene sets to.
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 #' If this collection already exists in \code{inSCE}, then these gene sets will
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@@ -37,7 +37,7 @@
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 #' \link{importGeneSetsFromMSigDB} for importing MSigDB gene sets.
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 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object
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 #'  with gene set from \code{collectionName} output stored to the
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-#'  \link[S4Vectors]{metadata} slot.
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+#'  \link{metadata} slot.
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 #' @examples
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 #' data(scExample)
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 #'
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@@ -92,7 +92,7 @@ importGeneSetsFromGMT <- function(inSCE, file,
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 #' Default \code{"rownames"}.
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 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object
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 #' with gene set from \code{collectionName} output stored to the
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-#' \link[S4Vectors]{metadata} slot.
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+#' \link{metadata} slot.
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 #' @details The gene identifiers in gene sets in \code{geneSetList} will be
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 #' mapped to the rownames of \code{inSCE} using the \code{by} parameter and
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 #' stored in a \linkS4class{GeneSetCollection} object from package
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@@ -169,7 +169,7 @@ importGeneSetsFromList <- function(inSCE, geneSetList,
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 #' downstream quality control and analysis functions in \link{singleCellTK}.
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 #' @param inSCE Input \linkS4class{SingleCellExperiment} object.
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 #' @param geneSetCollection A \linkS4class{GeneSetCollection} object. See
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-#' \link[GSEABase]{GeneSetCollection} for more details.
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+#' \link{GeneSetCollection} for more details.
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 #' @param collectionName Character. Name of collection to add gene sets to.
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 #' If this collection already exists in \code{inSCE}, then these gene sets will
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 #' be added to that collection. Any gene sets within the collection with the
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@@ -190,7 +190,7 @@ importGeneSetsFromList <- function(inSCE, geneSetList,
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 #' Default \code{"rownames"}.
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 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object
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 #' with gene set from \code{collectionName} output stored to the
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-#' \link[S4Vectors]{metadata} slot.
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+#' \link{metadata} slot.
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 #' @details The gene identifiers in gene sets in the
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 #' \code{GeneSetCollection} will be mapped to the rownames of
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 #' \code{inSCE} using the \code{by} parameter and
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@@ -315,7 +315,7 @@ importGeneSetsFromCollection <- function(inSCE, geneSetCollection,
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 #' @param verbose Boolean. Whether to display progress. Default \code{TRUE}.
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 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object
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 #' with gene set from \code{collectionName} output stored to the
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-#' \link[S4Vectors]{metadata} slot.
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+#' \link{metadata} slot.
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 #' @details The gene identifiers in gene sets from MSigDB will be retrieved
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 #' using the \code{\link{msigdbr}} package. They will be mapped to the IDs in
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 #' \code{inSCE} using the \code{by} parameter and
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@@ -2,7 +2,7 @@
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 #' Imports samples from different sources and compiles them into a list of SCE objects
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 #' @param allImportEntries object containing the sources and parameters of all the samples being imported (from the UI)
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.
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+#'  \link{DelayedArray} object or not. Default \code{TRUE}.
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 #' @return A list of \link[SingleCellExperiment]{SingleCellExperiment} object containing
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 #' the droplet or cell data or both,depending on the dataType that users provided.
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 #' @export
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@@ -243,10 +243,10 @@
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 #'  optimus_v1.4.0.
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 #' @param class Character. The class of the expression matrix stored in the SCE
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 #'  object. Can be one of "Matrix" (as returned by
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-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by
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+#'  \link{readMM} function), or "matrix" (as returned by
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 #'  \link[base]{matrix} function). Default "Matrix".
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.
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+#'  \link{DelayedArray} object or not. Default \code{TRUE}.
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 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object
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 #'  containing the count
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 #'  matrix, the gene annotation, and the cell annotation.
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@@ -107,10 +107,10 @@
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 #'  length as \code{samples}.
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 #' @param class Character. The class of the expression matrix stored in the SCE
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 #'  object. Can be one of "Matrix" (as returned by
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-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by
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+#'  \link{readMM} function), or "matrix" (as returned by
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 #'  \link[base]{matrix} function). Default "Matrix".
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.
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+#'  \link{DelayedArray} object or not. Default \code{TRUE}.
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 #' @return A \code{SingleCellExperiment} object containing the count
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 #'  matrix, the gene annotation, and the cell annotation.
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 #' @examples
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@@ -164,10 +164,10 @@
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 #' Default \code{FALSE}.
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 #' @param class Character. The class of the expression matrix stored in the SCE
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 #'  object. Can be one of "Matrix" (as returned by
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-#'  \link[Matrix]{readMM} function), or "matrix" (as returned by
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+#'  \link{readMM} function), or "matrix" (as returned by
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 #'  \link[base]{matrix} function). Default "Matrix".
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.
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+#'  \link{DelayedArray} object or not. Default \code{TRUE}.
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 #' @param feNotFirstCol Boolean. \code{TRUE} if first column of
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 #'  sparse_counts_genes.csv
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 #' is row index and it will be removed. \code{FALSE} the first column will
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@@ -40,7 +40,7 @@
40 40
 #' @param axis Choose from \code{"col"} or \code{"row"}.
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 #' @param colorGen A function that generates color code vector by giving an
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 #' integer for the number of colors. Alternatively,
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-#' \code{\link[grDevices]{rainbow}}. Default \code{\link{distinctColors}}.
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+#' \code{\link{rainbow}}. Default \code{\link{distinctColors}}.
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 #' @return A \code{list} object containing distinct colors mapped to all
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 #' possible categorical entries in \code{rowData(inSCE)} or
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 #' \code{colData(inSCE)}.
... ...
@@ -36,14 +36,14 @@
36 36
 #'  will convert to a sparse format which should be used
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 #'  for datasets with large numbers of cells.  Default "Matrix".
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 #' @param delayedArray Boolean. Whether to read the expression matrix as
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-#'  \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.
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+#'  \link{DelayedArray} object or not. Default \code{TRUE}.
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 #' @param colIndexLocation Character. For Optimus output, the path to the
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 #'  barcode index .npy file. Used only if \code{file} has .npz extension.
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 #'  Default \code{NULL}.
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 #' @param rowIndexLocation Character. For Optimus output, The path to the
44 44
 #'  feature (gene) index .npy file. Used only if \code{file} has .npz extension.
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 #'  Default \code{NULL}.
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-#' @return A \link[DelayedArray]{DelayedArray} object or matrix.
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+#' @return A \link{DelayedArray} object or matrix.
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 #' @examples
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 #' mat <- readSingleCellMatrix(system.file("extdata/hgmm_1k_v3_20x20/outs/",
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 #'     "filtered_feature_bc_matrix/matrix.mtx.gz", package = "singleCellTK"))
... ...
@@ -30,7 +30,7 @@ ad <- NULL
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 #' @name sctkPythonInstallConda
31 31
 #' @title Installs Python packages into a Conda environment
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 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package
33
-#' using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This
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+#' using \code{\link{conda_install}} from package \code{\link{reticulate}}. This
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 #' will create a new Conda environment with the name \code{envname} if not already present.
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 #' Note that Anaconda or Miniconda already need to be installed on the local system.
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 #' @param envname Character. Name of the conda environment to create.
... ...
@@ -42,15 +42,15 @@ ad <- NULL
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 #' @param pipIgnoreInstalled Boolean. Ignore installed versions when using pip. This is TRUE by default so that specific package versions can be installed even if they are downgrades.
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 #'        The FALSE option is useful for situations where you don't want a pip install to attempt an overwrite of a conda binary package (e.g. SciPy on Windows which is very difficult
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 #'        to install via pip due to compilation requirements).
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-#' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL.
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-#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}.
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+#' @param pythonVersion Passed to \code{python_version} variable in \code{\link{conda_install}}. Default NULL.
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+#' @param ... Other parameters to pass to \code{\link{conda_install}}.
47 47
 #' @return None. Installation of Conda environment.
48 48
 #' @examples
49 49
 #' \dontrun{
50 50
 #' sctkPythonInstallConda(envname = "sctk-reticulate")
51 51
 #' }
52
-#' @seealso See \code{\link[reticulate]{conda_create}} for more information on creating a Conda environment.
53
-#' See \code{\link[reticulate]{conda_install}} for more description of the installation parameters.
52
+#' @seealso See \code{\link{conda_create}} for more information on creating a Conda environment.
53
+#' See \code{\link{conda_install}} for more description of the installation parameters.
54 54
 #' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
55 55
 #' See \code{\link[singleCellTK]{selectSCTKConda}} for reloading the Conda environment if R is restarted without
56 56
 #' going through the whole installation process again.
... ...
@@ -88,7 +88,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",
88 88
 #' @name sctkPythonInstallVirtualEnv
89 89
 #' @title Installs Python packages into a virtual environment
90 90
 #' @description Install all Python packages used in the \code{\link{singleCellTK}} package
91
-#' using \code{\link[reticulate]{virtualenv_install}} from package \code{\link{reticulate}}. This
91
+#' using \code{\link{virtualenv_install}} from package \code{\link{reticulate}}. This
92 92
 #' will create a new virtual environment with the name \code{envname} if not already present.
93 93
 #' @param envname Character. Name of the virtual environment to create.
94 94
 #' @param packages Character Vector. List of packages to install.
... ...
@@ -99,8 +99,8 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",
99 99
 #' \dontrun{
100 100
 #' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")
101 101
 #' }
102
-#' @seealso See \code{\link[reticulate]{virtualenv_create}} for more information on creating a Conda environment.
103
-#' See \code{\link[reticulate]{virtualenv_install}} for more description of the installation parameters.
102
+#' @seealso See \code{\link{virtualenv_create}} for more information on creating a Conda environment.
103
+#' See \code{\link{virtualenv_install}} for more description of the installation parameters.
104 104
 #' See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
105 105
 #' See \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} for reloading the virtual environment if R is restarted without
106 106
 #' going through the whole installation process again.
... ...
@@ -7,7 +7,7 @@
7 7
 #' @param useAssay A single character indicating the name of the assay requiring
8 8
 #' batch correction. Default \code{"logcounts"}.
9 9
 #' @param batch A single character indicating a field in
10
-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.
10
+#' \code{\link{colData}} that annotates the batches.
11 11
 #' Default \code{"batch"}.
12 12
 #' @param reducedDimName A single character. The name for the corrected
13 13
 #' low-dimensional representation. Will be saved to \code{reducedDim(inSCE)}.
... ...
@@ -71,7 +71,7 @@ runBBKNN <-function(inSCE, useAssay = 'logcounts', batch = 'batch',
71 71
 #' @param useAssay A single character indicating the name of the assay requiring
72 72
 #' batch correction. Default \code{"logcounts"}.
73 73
 #' @param batch A single character indicating a field in
74
-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.
74
+#' \code{\link{colData}} that annotates the batches.
75 75
 #' Default \code{"batch"}.
76 76
 #' @param par.prior A logical scalar. TRUE indicates parametric adjustments
77 77
 #' will be used, FALSE indicates non-parametric adjustments will be used.
... ...
@@ -83,7 +83,7 @@ runBBKNN <-function(inSCE, useAssay = 'logcounts', batch = 'batch',
83 83
 #' @param ref.batch If given, will use the selected batch as a reference for
84 84
 #' batch adjustment. Default \code{NULL}.
85 85
 #' @param assayName A single characeter. The name for the corrected assay. Will
86
-#' be saved to \code{\link[SummarizedExperiment]{assay}}. Default
86
+#' be saved to \code{\link{assay}}. Default
87 87
 #' \code{"ComBat"}.
88 88
 #' @return The input \linkS4class{SingleCellExperiment} object with
89 89
 #' \code{assay(inSCE, assayName)} updated.
... ...
@@ -143,7 +143,7 @@ runComBat <- function(inSCE, useAssay = "logcounts", batch = 'batch',
143 143
 #' batch correction. Default \code{"logcounts"}. Alternatively, see
144 144
 #' \code{pcInput} parameter.
145 145
 #' @param batch A single character indicating a field in
146
-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.
146
+#' \code{\link{colData}} that annotates the batches.
147 147
 #' Default \code{"batch"}.
148 148
 #' @param reducedDimName A single character. The name for the corrected
149 149
 #' low-dimensional representation. Will be saved to \code{reducedDim(inSCE)}.
... ...
@@ -208,7 +208,7 @@ runFastMNN <- function(inSCE, useAssay = "logcounts",
208 208
 # #' @param useAssay A single character indicating the name of the assay requiring
209 209
 # #' batch correction. Default \code{"logcounts"}.
210 210
 # #' @param batch A single character indicating a field in
211
-# #' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.
211
+# #' \code{\link{colData}} that annotates the batches.
212 212
 # #' Default \code{"batch"}.
213 213
 # #' @param reducedDimName A single character. The name for the corrected
214 214
 # #' low-dimensional representation. Will be saved to \code{reducedDim(inSCE)}.
... ...
@@ -282,7 +282,7 @@ runFastMNN <- function(inSCE, useAssay = "logcounts",
282 282
 # #' @param useAssay A single character indicating the name of the assay requiring
283 283
 # #' batch correction. Default \code{"logcounts"}.
284 284
 # #' @param batch A single character indicating a field in
285
-# #' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.
285
+# #' \code{\link{colData}} that annotates the batches.
286 286
 # #' Default \code{"batch"}.
287 287
 # #' @param reducedDimName A single character. The name for the corrected
288 288
 # #' low-dimensional representation. Will be saved to \code{reducedDim(inSCE)}.
... ...
@@ -360,10 +360,10 @@ runFastMNN <- function(inSCE, useAssay = "logcounts",
360 360
 #' @param useAssay A single character indicating the name of the assay requiring
361 361
 #' batch correction. Default \code{"logcounts"}.
362 362
 #' @param batch A single character indicating a field in
363
-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.
363
+#' \code{\link{colData}} that annotates the batches.
364 364
 #' Default \code{"batch"}.
365 365
 #' @param assayName A single characeter. The name for the corrected assay. Will
366
-#' be saved to \code{\link[SummarizedExperiment]{assay}}. Default
366
+#' be saved to \code{\link{assay}}. Default
367 367
 #' \code{"LIMMA"}.
368 368
 #' @return The input \linkS4class{SingleCellExperiment} object with
369 369
 #' \code{assay(inSCE, assayName)} updated.
... ...
@@ -408,7 +408,7 @@ runLimmaBC <- function(inSCE, useAssay = "logcounts", assayName = "LIMMA",
408 408
 #' @param useAssay A single character indicating the name of the assay requiring
409 409
 #' batch correction. Default \code{"logcounts"}.
410 410
 #' @param batch A single character indicating a field in
411
-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.
411
+#' \code{\link{colData}} that annotates the batches.
412 412
 #' Default \code{"batch"}.
413 413
 #' @param k An integer. Specifies the number of nearest neighbours to
414 414
 #' consider when defining MNN pairs. This should be interpreted as the minimum
... ...
@@ -423,7 +423,7 @@ runLimmaBC <- function(inSCE, useAssay = "logcounts", assayName = "LIMMA",
423 423
 #' which may be more accurate but comes at the cost of precision. Default
424 424
 #' \code{0.1}.
425 425
 #' @param assayName A single characeter. The name for the corrected assay. Will
426
-#' be saved to \code{\link[SummarizedExperiment]{assay}}. Default
426
+#' be saved to \code{\link{assay}}. Default
427 427
 #' \code{"MNN"}.
428 428
 #' @return The input \linkS4class{SingleCellExperiment} object with
429 429
 #' \code{assay(inSCE, assayName)} updated.
... ...
@@ -467,7 +467,7 @@ runMNNCorrect <- function(inSCE, useAssay = 'logcounts', batch = 'batch',
467 467
 #' @param useAssay A single character indicating the name of the assay requiring
468 468
 #' batch correction. Default \code{"logcounts"}.
469 469
 #' @param batch A single character indicating a field in
470
-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.
470
+#' \code{\link{colData}} that annotates the batches.
471 471
 #' Default \code{"batch"}.
472 472
 #' @param SIGMA A numeric scalar. Algorithmic parameter, correction smoothing
473 473
 #' parameter on Gaussian kernel. Default \code{15}.
... ...
@@ -476,7 +476,7 @@ runMNNCorrect <- function(inSCE, useAssay = 'logcounts', batch = 'batch',
476 476
 #' @param KNN An integer. Algorithmic parameter, number of nearest neighbors to
477 477
 #' use for matching. Default \code{20L}.
478 478
 #' @param assayName A single characeter. The name for the corrected assay. Will
479
-#' be saved to \code{\link[SummarizedExperiment]{assay}}. Default
479
+#' be saved to \code{\link{assay}}. Default
480 480
 #' \code{"SCANORAMA"}.
481 481
 #' @return The input \linkS4class{SingleCellExperiment} object with
482 482
 #' \code{assay(inSCE, assayName)} updated.
... ...
@@ -558,7 +558,7 @@ integrated = integrated[:, orderIdx]
558 558
 #' @param useAssay A single character indicating the name of the assay requiring
559 559
 #' batch correction. Default \code{"logcounts"}.
560 560
 #' @param batch A single character indicating a field in
561
-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.
561
+#' \code{\link{colData}} that annotates the batches.
562 562
 #' Default \code{"batch"}.
563 563
 #' @param kmeansK An integer vector. Indicating the kmeans' K-value for each
564 564
 #' batch (i.e. how many subclusters in each batch should exist), in order to
... ...
@@ -576,7 +576,7 @@ integrated = integrated[:, orderIdx]
576 576
 #' @param nCores An integer. The number of cores of processors to allocate for
577 577
 #' the task. Default \code{1L}.
578 578
 #' @param assayName A single characeter. The name for the corrected assay. Will
579
-#' be saved to \code{\link[SummarizedExperiment]{assay}}. Default
579
+#' be saved to \code{\link{assay}}. Default
580 580
 #' \code{"scMerge"}.
581 581
 #' @return The input \linkS4class{SingleCellExperiment} object with
582 582
 #' \code{assay(inSCE, assayName)} updated.
... ...
@@ -672,7 +672,7 @@ runSCMerge <- function(inSCE, useAssay = "logcounts", batch = 'batch',
672 672
 #' batch correction. Note that ZINBWaVE works for counts (integer) input rather
673 673
 #' than logcounts that other methods prefer. Default \code{"counts"}.
674 674
 #' @param batch A single character indicating a field in
675
-#' \code{\link[SummarizedExperiment]{colData}} that annotates the batches.
675
+#' \code{\link{colData}} that annotates the batches.
676 676
 #' Default \code{"batch"}.
677 677
 #' @param nHVG An integer. Number of highly variable genes to use when fitting
678 678
 #' the model. Default \code{1000L}.
... ...
@@ -16,7 +16,7 @@
16 16
 #' @param seed Seed for the random number generator. Default 12345.
17 17
 #' @param paramsList A list containing parameters for QC functions. Default NULL.
18 18
 #' @return SingleCellExperiment object containing the outputs of the
19
-#'  specified algorithms in the \link[SummarizedExperiment]{colData}
19
+#'  specified algorithms in the \link{colData}
20 20
 #' of \code{inSCE}.
21 21
 #' @examples
22 22
 #' data(scExample, package = "singleCellTK")
... ...
@@ -137,7 +137,7 @@ runCellQC <- function(inSCE,
137 137
 #'  matrix for droplets.
138 138
 #' @param paramsList A list containing parameters for QC functions. Default NULL.
139 139
 #' @return SingleCellExperiment object containing the outputs of the
140
-#'  specified algorithms in the \link[SummarizedExperiment]{colData}
140
+#'  specified algorithms in the \link{colData}
141 141
 #' of \code{inSCE}.
142 142
 #' @examples
143 143
 #' data(scExample, package = "singleCellTK")
... ...
@@ -110,8 +110,7 @@
110 110
 #' @description  Creates a table of QC metrics generated from
111 111
 #'  QC algorithms via either kable or csv file.
112 112
 #' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved
113
-#' \link[SummarizedExperiment]{assay} data and/or
114
-#' \link[SummarizedExperiment]{colData} data. Required.
113
+#' \link{assay} data and/or \link{colData} data. Required.
115 114
 #' @param sample Character vector. Indicates which sample each cell belongs to.
116 115
 #' @param useAssay  A string specifying which assay in the SCE to use. Default
117 116
 #'  'counts'.
... ...
@@ -9,7 +9,7 @@
9 9
 #' If another character is supplied, then genes will be looked up in the column names of \code{rowData(inSCE)}. A character vector with the same length as \code{geneSetList} can be supplied if the IDs for different
10 10
 #' gene sets are found in different places, including a mixture of 'rownames' and \code{rowData(inSCE)}. An integer or integer vector can be supplied to denote the column index in \code{rowData(inSCE)}. Default 'rownames'.
11 11
 #' @param geneSetCollection Class of \code{GeneSetCollection} from package \code{GSEAbase}. The location of the gene IDs in \code{inSCE} should be in the \code{description} slot of each gene set and should follow the
12
-#' same notation as \code{geneSetListLocation}. The function \link[GSEABase]{getGmt} can be used to read in gene sets from a GMT file. If reading a GMT file, the second column for each gene set should be the description denoting the location
12
+#' same notation as \code{geneSetListLocation}. The function \link{getGmt} can be used to read in gene sets from a GMT file. If reading a GMT file, the second column for each gene set should be the description denoting the location
13 13
 #' of the gene IDs in \code{inSCE}. These gene sets will be included with those from \code{geneSetList} if both parameters are provided.
14 14
 #' @param percent_top An integer vector. Each element is treated as a
15 15
 #' number of top genes to compute the percentage of library size occupied by
... ...
@@ -23,10 +23,10 @@
23 23
 #' @param flatten Logical scalar indicating whether the nested \link[S4Vectors]{DataFrame-class}
24 24
 #' in the output should be flattened.
25 25
 #' @param detectionLimit A numeric scalar specifying the lower detection limit for expression.
26
-#' @param BPPARAM A \link[BiocParallel]{BiocParallelParam} object specifying
26
+#' @param BPPARAM A \link{BiocParallelParam} object specifying
27 27
 #' whether the QC calculations should be parallelized.
28 28
 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with
29
-#'  cell QC metrics added to the \link[SummarizedExperiment]{colData} slot. If \code{geneSetList} or \code{geneSetCollection} are provided, then the rownames for each gene set will be saved in \code{metadata(inSCE)$scater$addPerCellQC$geneSets}.
29
+#'  cell QC metrics added to the \link{colData} slot. If \code{geneSetList} or \code{geneSetCollection} are provided, then the rownames for each gene set will be saved in \code{metadata(inSCE)$scater$addPerCellQC$geneSets}.
30 30
 #' @examples
31 31
 #' data(scExample, package = "singleCellTK")
32 32
 #' mito.ix = grep("^MT-", rowData(sce)$feature_name)
... ...
@@ -1,5 +1,5 @@
1 1
 #' scater_logNormCounts
2
-#' Uses \link[scater]{logNormCounts} to log normalize input data
2
+#' Uses \link{logNormCounts} to log normalize input data
3 3
 #' @param inSCE Input SingleCellExperiment object
4 4
 #' @param logAssayName New assay name for log normalized data
5 5
 #' @param useAssay Input assay 
... ...
@@ -18,7 +18,7 @@
18 18
 #' @param useAssay  A string specifying which assay in the SCE to use.
19 19
 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with
20 20
 #'  \link[scds]{cxds} output appended to the
21
-#'  \link[SummarizedExperiment]{colData} slot. The columns include
21
+#'  \link{colData} slot. The columns include
22 22
 #'  \emph{cxds_score} and optionally \emph{cxds_call}.
23 23
 #'  Please refer to the documentation of \link[scds]{cxds} for details.
24 24
 #' @examples
... ...
@@ -130,7 +130,7 @@ runCxds <- function(inSCE,
130 130
 #' @param useAssay  A string specifying which assay in the SCE to use.
131 131
 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with
132 132
 #'  \link[scds]{bcds} output appended to the
133
-#'  \link[SummarizedExperiment]{colData} slot. The columns include
133
+#'  \link{colData} slot. The columns include
134 134
 #'  \emph{bcds_score} and optionally \emph{bcds_call}.
135 135
 #'  Please refer to the documentation of \link[scds]{bcds} for details.
136 136
 #' @examples
... ...
@@ -250,7 +250,7 @@ runBcds <- function(inSCE,
250 250
 #' @param useAssay  A string specifying which assay in the SCE to use.
251 251
 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with
252 252
 #'  \link[scds]{cxds_bcds_hybrid} output appended to the
253
-#'  \link[SummarizedExperiment]{colData} slot. The columns include
253
+#'  \link{colData} slot. The columns include
254 254
 #'  \emph{hybrid_score} and optionally \emph{hybrid_call}.
255 255
 #'  Please refer to the documentation of \link[scds]{cxds_bcds_hybrid} for
256 256
 #'  details.
... ...
@@ -72,16 +72,16 @@
72 72
 #' This should be an algorithm supported by \code{\link[BiocNeighbors]{findNeighbors}}.
73 73
 #' @param BSPARAM A \code{\link[BiocSingular]{BiocSingularParam}} object specifying the algorithm to
74 74
 #'  use for PCA, if \code{d} is not \code{NA}.
75
-#' @param BPPARAM A \code{\link[BiocParallel]{BiocParallelParam}} object specifying whether the
75
+#' @param BPPARAM A \code{\link{BiocParallelParam}} object specifying whether the
76 76
 #'  neighbour searches should be parallelized.
77 77
 #' @details This function is a wrapper function for \link[scran]{doubletCells}.
78 78
 #'  \code{runDoubletCells} runs \link[scran]{doubletCells} for each
79 79
 #'  \code{sample} within \code{inSCE} iteratively. The
80 80
 #'  resulting doublet scores for all cells will be appended to the
81
-#'  \link[SummarizedExperiment]{colData} of \code{inSCE}.
81
+#'  \link{colData} of \code{inSCE}.
82 82
 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with the
83 83
 #'  'scran_doubletCells_score' column added to the
84
-#'  \link[SummarizedExperiment]{colData} slot.
84
+#'  \link{colData} slot.
85 85
 #' @references Lun ATL (2018). Detecting doublet cells with scran.
86 86
 #'  \url{https://ltla.github.io/SingleCellThoughts/software/
87 87
 #' doublet_detection/bycell.html}
... ...
@@ -75,7 +75,7 @@
75 75
 #' @param seed Seed for the random number generator. Default 12345.
76 76
 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with
77 77
 #'  \code{scrub_doublets} output appended to the
78
-#'  \link[SummarizedExperiment]{colData} slot. The columns include
78
+#'  \link{colData} slot. The columns include
79 79
 #'  \emph{scrublet_score} and \emph{scrublet_call}.
80 80
 #' @examples
81 81
 #' data(scExample, package = "singleCellTK")
... ...
@@ -494,7 +494,7 @@ seuratHeatmapPlot <- function(plotObject, dims, ncol, labels) {
494 494
 #' @param seuratDataSlot Selected data slot from the Seurat object. Default \code{"counts"}.
495 495
 #' @param seuratAssaySlot Selected assay from Seurat object. Default \code{"RNA"}.
496 496
 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with
497
-#'  data from Seurat object appended to the \link[SummarizedExperiment]{assay} slot.
497
+#'  data from Seurat object appended to the \link{assay} slot.
498 498
 #' @importFrom SummarizedExperiment assay<-
499 499
 .updateAssaySCE <- function(inSCE, seuratObject, assaySlotSCE, seuratDataSlot = "counts", seuratAssaySlot = "RNA") {
500 500
   assay(inSCE, assaySlotSCE) <- NULL
... ...
@@ -6,7 +6,7 @@
6 6
 #' with one another. If \code{returnAsAltExp} is set to \code{TRUE},
7 7
 #' then the returned object will have the same number of rows as the input
8 8
 #' \code{inSCE} as the subsetted object will be stored in the
9
-#' \code{\link[SingleCellExperiment]{altExp}} slot.
9
+#' \code{\link{altExp}} slot.
10 10
 #' @param inSCE Input \linkS4class{SingleCellExperiment} object.
11 11
 #' @param index Integer vector. Vector of indicies indicating which rows
12 12
 #' to keep. If \code{NULL}, this will not be used for subsetting.
... ...
@@ -15,7 +15,7 @@ dataAnnotationColor(inSCE, axis = NULL, colorGen = distinctColors)
15 15
 
16 16
 \item{colorGen}{A function that generates color code vector by giving an
17 17
 integer for the number of colors. Alternatively,
18
-\code{\link[grDevices]{rainbow}}. Default \code{\link{distinctColors}}.}
18
+\code{\link{rainbow}}. Default \code{\link{distinctColors}}.}
19 19
 }
20 20
 \value{
21 21
 A \code{list} object containing distinct colors mapped to all
... ...
@@ -26,7 +26,7 @@ Update/Modify/Add an assay in the provided SingleCellExperiment object from a Se
26 26
 }
27 27
 \value{
28 28
 A \link[SingleCellExperiment]{SingleCellExperiment} object with
29
- data from Seurat object appended to the \link[SummarizedExperiment]{assay} slot.
29
+ data from Seurat object appended to the \link{assay} slot.
30 30
 }
31 31
 \description{
32 32
 .updateAssaySCE
... ...
@@ -33,13 +33,13 @@ selected.variable features. Default \code{NULL}.}
33 33
 
34 34
 \item{sample}{Character vector. Indicates which sample each cell belongs to.
35 35
 If given a single character, will take the annotation from
36
-\code{\link[SummarizedExperiment]{colData}}. Default \code{NULL}.}
36
+\code{\link{colData}}. Default \code{NULL}.}
37 37
 
38 38
 \item{reducedDimName}{A name to store the results of the dimension reduction
39 39
 coordinates obtained from this method. Default \code{"UMAP"}.}
40 40
 
41 41
 \item{logNorm}{Whether the counts will need to be log-normalized prior to
42
-generating the UMAP via \code{\link[scater]{logNormCounts}}. Default
42
+generating the UMAP via \code{\link{logNormCounts}}. Default
43 43
 \code{TRUE}.}
44 44
 
45 45
 \item{nNeighbors}{The size of local neighborhood used for manifold
... ...
@@ -60,7 +60,7 @@ result on a more even dispersal of points. Default \code{0.01}. See
60 60
 `?uwot::umap` for more information.}
61 61
 
62 62
 \item{spread}{The effective scale of embedded points. In combination with
63
-‘min_dist’, this determines how clustered/clumped the embedded points are.
63
+minDist, this determines how clustered/clumped the embedded points are.
64 64
 Default \code{1}. See `?uwot::umap` for more information.}
65 65
 
66 66
 \item{pca}{Logical. Whether to perform dimension reduction with PCA before
... ...
@@ -30,7 +30,7 @@ Can be one of -
30 30
 }}
31 31
 
32 32
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
33
-\link[DelayedArray]{DelayedArray} object. Default \code{TRUE}.}
33
+\link{DelayedArray} object. Default \code{TRUE}.}
34 34
 }
35 35
 \value{
36 36
 A \code{SingleCellExperiment} object.
... ...
@@ -42,11 +42,11 @@ files are gzip compressed. Must have length 1 or the same length as
42 42
 
43 43
 \item{class}{Character. The class of the expression matrix stored in the SCE
44 44
 object. Can be one of "Matrix" (as returned by
45
-\link[Matrix]{readMM} function), or "matrix" (as returned by
45
+\link{readMM} function), or "matrix" (as returned by
46 46
 \link[base]{matrix} function). Default "Matrix".}
47 47
 
48 48
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
49
-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
49
+\link[DelayedArray]{DelayedArray-class} object or not. Default \code{TRUE}.}
50 50
 }
51 51
 \value{
52 52
 A \code{SingleCellExperiment} object containing the count
... ...
@@ -50,7 +50,7 @@ argument.}
50 50
 \itemize{
51 51
   \item \code{NULL}. All samples within \code{cellRangerDirs} will be
52 52
    imported. The order of samples will be first determined by the order of
53
-   \code{cellRangerDirs} and then by \link[base]{list.dirs}. This is only
53
+   \code{cellRangerDirs} and then by \link{list.dirs}. This is only
54 54
    for the case where \code{cellRangerDirs} is specified.
55 55
   \item A list of vectors containing the folder names for samples to import.
56 56
    Each vector in
... ...
@@ -134,11 +134,11 @@ order match the output of
134 134
 
135 135
 \item{class}{Character. The class of the expression matrix stored in the SCE
136 136
 object. Can be one of "Matrix" (as returned by
137
-\link[Matrix]{readMM} function), or "matrix" (as returned by
137
+\link{readMM} function), or "matrix" (as returned by
138 138
 \link[base]{matrix} function). Default \code{"Matrix"}.}
139 139
 
140 140
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
141
-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
141
+\link{DelayedArray} object or not. Default \code{TRUE}.}
142 142
 
143 143
 \item{dataTypeV2}{Character. The type of output to import for
144 144
 Cellranger version below 3.0.0. Whether to import the filtered or the 
... ...
@@ -19,11 +19,11 @@ Default "sample".}
19 19
 
20 20
 \item{class}{Character. The class of the expression matrix stored in the SCE
21 21
 object. Can be one of "Matrix" (as returned by
22
-\link[Matrix]{readMM} function), or "matrix" (as returned by
22
+\link{readMM} function), or "matrix" (as returned by
23 23
 \link[base]{matrix} function). Default "Matrix".}
24 24
 
25 25
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
26
-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
26
+\link{DelayedArray} object or not. Default \code{TRUE}.}
27 27
 }
28 28
 \value{
29 29
 A \code{SingleCellExperiment} object containing the count
... ...
@@ -19,11 +19,11 @@ Default "sample".}
19 19
 
20 20
 \item{class}{Character. The class of the expression matrix stored in the SCE
21 21
 object. Can be one of "Matrix" (as returned by
22
-\link[Matrix]{readMM} function), or "matrix" (as returned by
22
+\link{readMM} function), or "matrix" (as returned by
23 23
 \link[base]{matrix} function). Default "Matrix".}
24 24
 
25 25
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
26
-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
26
+\link{DelayedArray} object or not. Default \code{TRUE}.}
27 27
 }
28 28
 \value{
29 29
 A \code{SingleCellExperiment} object containing the count
... ...
@@ -23,7 +23,7 @@ importDropEst(
23 23
 Default "sample".}
24 24
 
25 25
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
26
-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
26
+\link{DelayedArray} object or not. Default \code{TRUE}.}
27 27
 }
28 28
 \value{
29 29
 A \code{SingleCellExperiment} object containing the count matrix,
... ...
@@ -16,7 +16,7 @@ will store the data as a sparse matrix from package \link{Matrix} while
16 16
 \code{"Matrix"}.}
17 17
 
18 18
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
19
-\link[DelayedArray]{DelayedArray} object or not. Default \code{FALSE}.}
19
+\link{DelayedArray} object or not. Default \code{FALSE}.}
20 20
 }
21 21
 \value{
22 22
 The specified \link[SingleCellExperiment]{SingleCellExperiment} object.
... ...
@@ -24,7 +24,7 @@ The specified \link[SingleCellExperiment]{SingleCellExperiment} object.
24 24
 \description{
25 25
 Retrieves published example datasets stored in
26 26
 \link[SingleCellExperiment]{SingleCellExperiment} using the
27
-\link[scRNAseq]{scRNAseq} and
27
+\link{scRNAseq} and
28 28
 \link[TENxPBMCData]{TENxPBMCData} packages. See 'Details' for a
29 29
 list of available datasets.
30 30
 }
... ...
@@ -33,11 +33,11 @@ See the list below for the available datasets and their
33 33
 descriptions.
34 34
 \describe{
35 35
 \item{"fluidigm_pollen"}{Retrieved with
36
-\code{\link[scRNAseq]{ReprocessedFluidigmData}}. Returns a dataset of 65
36
+\code{\link{ReprocessedFluidigmData}}. Returns a dataset of 65
37 37
  human neural cells from Pollen et al. (2014), each sequenced at high and low
38 38
  coverage (SRA accession SRP041736).}
39 39
 \item{"allen_tasic"}{Retrieved with
40
-\code{\link[scRNAseq]{ReprocessedAllenData}}. Returns a dataset of 379 mouse
40
+\code{\link{ReprocessedAllenData}}. Returns a dataset of 379 mouse
41 41
 brain cells from Tasic et al. (2016).}
42 42
 \item{"pbmc3k"}{Retrieved with \code{\link[TENxPBMCData]{TENxPBMCData}}.
43 43
  2,700 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.}
... ...
@@ -42,11 +42,11 @@ frames instead of file paths. The default is FALSE.}
42 42
 
43 43
 \item{class}{Character. The class of the expression matrix stored in the SCE
44 44
 object. Can be one of "Matrix" (as returned by
45
-\link[Matrix]{readMM} function), or "matrix" (as returned by
45
+\link{readMM} function), or "matrix" (as returned by
46 46
 \link[base]{matrix} function). Default "Matrix".}
47 47
 
48 48
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
49
-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
49
+\link{DelayedArray} object or not. Default \code{TRUE}.}
50 50
 
51 51
 \item{annotFileHeader}{Whether there's a header (colnames) in the cell annotation file. Default is FALSE}
52 52
 
... ...
@@ -15,7 +15,7 @@ importGeneSetsFromCollection(
15 15
 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object.}
16 16
 
17 17
 \item{geneSetCollection}{A \linkS4class{GeneSetCollection} object. See
18
-\link[GSEABase]{GeneSetCollection} for more details.}
18
+\link{GeneSetCollection} for more details.}
19 19
 
20 20
 \item{collectionName}{Character. Name of collection to add gene sets to.
21 21
 If this collection already exists in \code{inSCE}, then these gene sets will
... ...
@@ -40,7 +40,7 @@ Default \code{"rownames"}.}
40 40
 \value{
41 41
 A \link[SingleCellExperiment]{SingleCellExperiment} object
42 42
 with gene set from \code{collectionName} output stored to the
43
-\link[S4Vectors]{metadata} slot.
43
+\link{metadata} slot.
44 44
 }
45 45
 \description{
46 46
 Converts a list of gene sets stored in a
... ...
@@ -15,7 +15,7 @@ importGeneSetsFromGMT(
15 15
 \arguments{
16 16
 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object.}
17 17
 
18
-\item{file}{Character. Path to GMT file. See \link[GSEABase]{getGmt} for
18
+\item{file}{Character. Path to GMT file. See \link{getGmt} for
19 19
 more information on reading GMT files.}
20 20
 
21 21
 \item{collectionName}{Character. Name of collection to add gene sets to.
... ...
@@ -42,7 +42,7 @@ Default \code{"rownames"}.}
42 42
 \value{
43 43
 A \link[SingleCellExperiment]{SingleCellExperiment} object
44 44
  with gene set from \code{collectionName} output stored to the
45
- \link[S4Vectors]{metadata} slot.
45
+ \link{metadata} slot.
46 46
 }
47 47
 \description{
48 48
 Converts a list of gene sets stored in a GMT file into a
... ...
@@ -39,7 +39,7 @@ Default \code{"rownames"}.}
39 39
 \value{
40 40
 A \link[SingleCellExperiment]{SingleCellExperiment} object
41 41
 with gene set from \code{collectionName} output stored to the
42
-\link[S4Vectors]{metadata} slot.
42
+\link{metadata} slot.
43 43
 }
44 44
 \description{
45 45
 Converts a list of gene sets into a
... ...
@@ -42,7 +42,7 @@ Default \code{"rownames"}.}
42 42
 \value{
43 43
 A \link[SingleCellExperiment]{SingleCellExperiment} object
44 44
 with gene set from \code{collectionName} output stored to the
45
-\link[S4Vectors]{metadata} slot.
45
+\link{metadata} slot.
46 46
 }
47 47
 \description{
48 48
 Gets a list of MSigDB gene sets stores it in the metadata of the
... ...
@@ -10,7 +10,7 @@ importMultipleSources(allImportEntries, delayedArray = FALSE)
10 10
 \item{allImportEntries}{object containing the sources and parameters of all the samples being imported (from the UI)}
11 11
 
12 12
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
13
-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
13
+\link{DelayedArray} object or not. Default \code{TRUE}.}
14 14
 }
15 15
 \value{
16 16
 A list of \link[SingleCellExperiment]{SingleCellExperiment} object containing
... ...
@@ -58,11 +58,11 @@ optimus_v1.4.0.}
58 58
 
59 59
 \item{class}{Character. The class of the expression matrix stored in the SCE
60 60
 object. Can be one of "Matrix" (as returned by
61
-\link[Matrix]{readMM} function), or "matrix" (as returned by
61
+\link{readMM} function), or "matrix" (as returned by
62 62
 \link[base]{matrix} function). Default "Matrix".}
63 63
 
64 64
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
65
-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
65
+\link{DelayedArray} object or not. Default \code{TRUE}.}
66 66
 }
67 67
 \value{
68 68
 A \link[SingleCellExperiment]{SingleCellExperiment} object
... ...
@@ -37,11 +37,11 @@ Default \code{FALSE}.}
37 37
 
38 38
 \item{class}{Character. The class of the expression matrix stored in the SCE
39 39
 object. Can be one of "Matrix" (as returned by
40
-\link[Matrix]{readMM} function), or "matrix" (as returned by
40
+\link{readMM} function), or "matrix" (as returned by
41 41
 \link[base]{matrix} function). Default "Matrix".}
42 42
 
43 43
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
44
-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
44
+\link{DelayedArray} object or not. Default \code{TRUE}.}
45 45
 
46 46
 \item{cbNotFirstCol}{Boolean. \code{TRUE} if first column of
47 47
  sparse_counts_barcode.csv
... ...
@@ -53,11 +53,11 @@ length as \code{samples}.}
53 53
 
54 54
 \item{class}{Character. The class of the expression matrix stored in the SCE
55 55
 object. Can be one of "Matrix" (as returned by
56
-\link[Matrix]{readMM} function), or "matrix" (as returned by
56
+\link{readMM} function), or "matrix" (as returned by
57 57
 \link[base]{matrix} function). Default "Matrix".}
58 58
 
59 59
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
60
-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
60
+\link{DelayedArray} object or not. Default \code{TRUE}.}
61 61
 }
62 62
 \value{
63 63
 A \code{SingleCellExperiment} object containing the count
... ...
@@ -23,7 +23,7 @@ will convert to a sparse format which should be used
23 23
 for datasets with large numbers of cells.  Default "Matrix".}
24 24
 
25 25
 \item{delayedArray}{Boolean. Whether to read the expression matrix as
26
-\link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}.}
26
+\link{DelayedArray} object or not. Default \code{TRUE}.}
27 27
 
28 28
 \item{colIndexLocation}{Character. For Optimus output, the path to the
29 29
 barcode index .npy file. Used only if \code{file} has .npz extension.
... ...
@@ -34,7 +34,7 @@ feature (gene) index .npy file. Used only if \code{file} has .npz extension.
34 34
 Default \code{NULL}.}
35 35
 }
36 36
 \value{
37
-A \link[DelayedArray]{DelayedArray} object or matrix.
37
+A \link{DelayedArray} object or matrix.
38 38
 }
39 39
 \description{
40 40
 Automatically detact the format of the input file and read
... ...
@@ -19,7 +19,7 @@ runBBKNN(
19 19
 batch correction. Default \code{"logcounts"}.}
20 20
 
21 21
 \item{batch}{A single character indicating a field in
22
-\code{\link[SummarizedExperiment]{colData}} that annotates the batches.
22
+\code{\link{colData}} that annotates the batches.
23 23
 Default \code{"batch"}.}
24 24
 
25 25
 \item{reducedDimName}{A single character. The name for the corrected
... ...
@@ -32,7 +32,7 @@ If NULL, then all cells will be processed together. Default \code{NULL}.}
32 32
 \value{
33 33
 A \link[SingleCellExperiment]{SingleCellExperiment} object with the
34 34
  \link[DropletUtils]{barcodeRanks} output table appended to the
35
- \link[SummarizedExperiment]{colData} slot. The columns include
35
+ \link{colData} slot. The columns include
36 36
  \emph{dropletUtils_BarcodeRank_Knee} and \emph{dropletUtils_BarcodeRank_Knee}
37 37
  Please refer to the documentation of \link[DropletUtils]{barcodeRanks} for
38 38
  details.
... ...
@@ -48,7 +48,7 @@ Default NULL.}
48 48
 \value{
49 49
 A \link[SingleCellExperiment]{SingleCellExperiment} object with
50 50
  \link[scds]{bcds} output appended to the
51
- \link[SummarizedExperiment]{colData} slot. The columns include
51
+ \link{colData} slot. The columns include
52 52
  \emph{bcds_score} and optionally \emph{bcds_call}.
53 53
  Please refer to the documentation of \link[scds]{bcds} for details.
54 54
 }
... ...
@@ -44,7 +44,7 @@ matrix for cells.}
44 44
 }
45 45
 \value{
46 46
 SingleCellExperiment object containing the outputs of the
47
- specified algorithms in the \link[SummarizedExperiment]{colData}
47
+ specified algorithms in the \link{colData}
48 48
 of \code{inSCE}.
49 49
 }
50 50
 \description{
... ...
@@ -22,7 +22,7 @@ runComBat(
22 22
 batch correction. Default \code{"logcounts"}.}
23 23
 
24 24
 \item{batch}{A single character indicating a field in
25
-\code{\link[SummarizedExperiment]{colData}} that annotates the batches.
25
+\code{\link{colData}} that annotates the batches.
26 26
 Default \code{"batch"}.}
27 27
 
28 28
 \item{par.prior}{A logical scalar. TRUE indicates parametric adjustments
... ...
@@ -39,7 +39,7 @@ Default \code{FALSE}.}
39 39
 batch adjustment. Default \code{NULL}.}
40 40
 
41 41
 \item{assayName}{A single characeter. The name for the corrected assay. Will
42
-be saved to \code{\link[SummarizedExperiment]{assay}}. Default
42
+be saved to \code{\link{assay}}. Default
43 43
 \code{"ComBat"}.}
44 44
 }
45 45
 \value{
... ...
@@ -42,7 +42,7 @@ Default NULL.}
42 42
 \value{
43 43
 A \link[SingleCellExperiment]{SingleCellExperiment} object with
44 44
  \link[scds]{cxds} output appended to the
45
- \link[SummarizedExperiment]{colData} slot. The columns include
45
+ \link{colData} slot. The columns include
46 46
  \emph{cxds_score} and optionally \emph{cxds_call}.
47 47
  Please refer to the documentation of \link[scds]{cxds} for details.
48 48
 }
... ...
@@ -46,7 +46,7 @@ and \code{bcds}. Default \code{500}.}
46 46
 \value{
47 47
 A \link[SingleCellExperiment]{SingleCellExperiment} object with
48 48
  \link[scds]{cxds_bcds_hybrid} output appended to the
49
- \link[SummarizedExperiment]{colData} slot. The columns include
49
+ \link{colData} slot. The columns include
50 50
  \emph{hybrid_score} and optionally \emph{hybrid_call}.
51 51
  Please refer to the documentation of \link[scds]{cxds_bcds_hybrid} for
52 52
  details.
... ...
@@ -87,7 +87,7 @@ a default value of 12345 is used. If NULL, no calls to
87 87
 \value{
88 88
 A \link[SingleCellExperiment]{SingleCellExperiment} object with
89 89
  'decontX_Contamination' and 'decontX_Clusters' added to the
90
- \link[SummarizedExperiment]{colData} slot. Additionally, the
90
+ \link{colData} slot. Additionally, the
91 91
 decontaminated counts will be added as an assay called 'decontXCounts'.
92 92
 }
93 93
 \description{
... ...
@@ -71,13 +71,13 @@ This should be an algorithm supported by \code{\link[BiocNeighbors]{findNeighbor
71 71
 \item{BSPARAM}{A \code{\link[BiocSingular]{BiocSingularParam}} object specifying the algorithm to
72 72
 use for PCA, if \code{d} is not \code{NA}.}
73 73
 
74
-\item{BPPARAM}{A \code{\link[BiocParallel]{BiocParallelParam}} object specifying whether the
74
+\item{BPPARAM}{A \code{\link{BiocParallelParam}} object specifying whether the
75 75
 neighbour searches should be parallelized.}
76 76
 }
77 77
 \value{
78 78
 A \link[SingleCellExperiment]{SingleCellExperiment} object with the
79 79
  'scran_doubletCells_score' column added to the
80
- \link[SummarizedExperiment]{colData} slot.
80
+ \link{colData} slot.
81 81
 }
82 82
 \description{
83 83
 A wrapper function for \link[scran]{doubletCells}. Identify
... ...
@@ -89,7 +89,7 @@ This function is a wrapper function for \link[scran]{doubletCells}.
89 89
  \code{runDoubletCells} runs \link[scran]{doubletCells} for each
90 90
  \code{sample} within \code{inSCE} iteratively. The
91 91
  resulting doublet scores for all cells will be appended to the
92
- \link[SummarizedExperiment]{colData} of \code{inSCE}.
92
+ \link{colData} of \code{inSCE}.
93 93
 }
94 94
 \examples{
95 95
 data(scExample, package = "singleCellTK")
... ...
@@ -29,7 +29,7 @@ matrix for droplets.}
29 29
 }
30 30
 \value{
31 31
 SingleCellExperiment object containing the outputs of the
32
- specified algorithms in the \link[SummarizedExperiment]{colData}
32
+ specified algorithms in the \link{colData}
33 33
 of \code{inSCE}.
34 34
 }
35 35
 \description{
... ...
@@ -47,7 +47,7 @@ If NULL, then all cells will be processed together. Default NULL.}
47 47
 \value{
48 48
 A \link[SingleCellExperiment]{SingleCellExperiment} object with the
49 49
  \link[DropletUtils]{emptyDrops} output table appended to the
50
- \link[SummarizedExperiment]{colData} slot. The columns include
50
+ \link{colData} slot. The columns include
51 51
  \emph{emptyDrops_total}, \emph{emptyDrops_logprob},
52 52
  \emph{emptyDrops_pvalue}, \emph{emptyDrops_limited}, \emph{emptyDrops_fdr}.
53 53
  Please refer to the documentation of \link[DropletUtils]{emptyDrops} for
... ...
@@ -25,7 +25,7 @@ low-dimensional representation. Will be saved to \code{reducedDim(inSCE)}.
25 25
 Default \code{"fastMNN"}.}
26 26
 
27 27
 \item{batch}{A single character indicating a field in
28
-\code{\link[SummarizedExperiment]{colData}} that annotates the batches.
28
+\code{\link{colData}} that annotates the batches.
29 29
 Default \code{"batch"}.}
30 30
 
31 31
 \item{pcInput}{A logical scalar. Whether to use a low-dimension matrix for
... ...
@@ -24,7 +24,7 @@ low-dimension representation to perform the clustering algorithm on. Default
24 24
 \code{"PCA"}.}
25 25
 
26 26
 \item{clusterName}{A single \code{character}, specifying the name to store
27
-the cluster label in \code{\link[SummarizedExperiment]{colData}}. Default
27
+the cluster label in \code{\link{colData}}. Default
28 28
 \code{"scranSNN_cluster"}.}
29 29
 
30 30
 \item{nCenters}{An \code{integer}, the number of centroids (clusters).}
... ...
@@ -13,11 +13,11 @@ runLimmaBC(inSCE, useAssay = "logcounts", assayName = "LIMMA", batch = "batch")
13 13
 batch correction. Default \code{"logcounts"}.}
14 14
 
15 15
 \item{assayName}{A single characeter. The name for the corrected assay. Will
16
-be saved to \code{\link[SummarizedExperiment]{assay}}. Default
16
+be saved to \code{\link{assay}}. Default
17 17
 \code{"LIMMA"}.}
18 18
 
19 19
 \item{batch}{A single character indicating a field in
20
-\code{\link[SummarizedExperiment]{colData}} that annotates the batches.
20
+\code{\link{colData}} that annotates the batches.
21 21
 Default \code{"batch"}.}
22 22
 }
23 23
 \value{
... ...
@@ -21,11 +21,11 @@ runMNNCorrect(
21 21
 batch correction. Default \code{"logcounts"}.}
22 22
 
23 23
 \item{batch}{A single character indicating a field in
24
-\code{\link[SummarizedExperiment]{colData}} that annotates the batches.
24
+\code{\link{colData}} that annotates the batches.
25 25
 Default \code{"batch"}.}
26 26
 
27 27
 \item{assayName}{A single characeter. The name for the corrected assay. Will
28
-be saved to \code{\link[SummarizedExperiment]{assay}}. Default
28
+be saved to \code{\link{assay}}. Default
29 29
 \code{"MNN"}.}
30 30
 
31 31
 \item{k}{An integer. Specifies the number of nearest neighbours to
... ...
@@ -32,7 +32,7 @@ If another character is supplied, then genes will be looked up in the column nam
32 32
 gene sets are found in different places, including a mixture of 'rownames' and \code{rowData(inSCE)}. An integer or integer vector can be supplied to denote the column index in \code{rowData(inSCE)}. Default 'rownames'.}
33 33
 
34 34
 \item{geneSetCollection}{Class of \code{GeneSetCollection} from package \code{GSEAbase}. The location of the gene IDs in \code{inSCE} should be in the \code{description} slot of each gene set and should follow the
35
-same notation as \code{geneSetListLocation}. The function \link[GSEABase]{getGmt} can be used to read in gene sets from a GMT file. If reading a GMT file, the second column for each gene set should be the description denoting the location
35
+same notation as \code{geneSetListLocation}. The function \link{getGmt} can be used to read in gene sets from a GMT file. If reading a GMT file, the second column for each gene set should be the description denoting the location
36 36
 of the gene IDs in \code{inSCE}. These gene sets will be included with those from \code{geneSetList} if both parameters are provided.}
37 37
 
38 38
 \item{percent_top}{An integer vector. Each element is treated as a
... ...
@@ -51,12 +51,12 @@ in the output should be flattened.}
51 51
 
52 52
 \item{detectionLimit}{A numeric scalar specifying the lower detection limit for expression.}
53 53
 
54
-\item{BPPARAM}{A \link[BiocParallel]{BiocParallelParam} object specifying
54
+\item{BPPARAM}{A \link{BiocParallelParam} object specifying
55 55
 whether the QC calculations should be parallelized.}
56 56
 }
57 57
 \value{
58 58
 A \link[SingleCellExperiment]{SingleCellExperiment} object with
59
- cell QC metrics added to the \link[SummarizedExperiment]{colData} slot. If \code{geneSetList} or \code{geneSetCollection} are provided, then the rownames for each gene set will be saved in \code{metadata(inSCE)$scater$addPerCellQC$geneSets}.
59
+ cell QC metrics added to the \link{colData} slot. If \code{geneSetList} or \code{geneSetCollection} are provided, then the rownames for each gene set will be saved in \code{metadata(inSCE)$scater$addPerCellQC$geneSets}.
60 60
 }
61 61
 \description{
62 62
 A wrapper function for \link[celda]{decontX}. Identify
... ...
@@ -22,7 +22,7 @@ runSCANORAMA(
22 22
 batch correction. Default \code{"logcounts"}.}
23 23
 
24 24
 \item{batch}{A single character indicating a field in
25
-\code{\link[SummarizedExperiment]{colData}} that annotates the batches.
25
+\code{\link{colData}} that annotates the batches.
26 26
 Default \code{"batch"}.}
27 27
 
28 28
 \item{SIGMA}{A numeric scalar. Algorithmic parameter, correction smoothing
... ...
@@ -35,7 +35,7 @@ minimum cutoff. Default \code{0.1}.}
35 35
 use for matching. Default \code{20L}.}
36 36
 
37 37
 \item{assayName}{A single characeter. The name for the corrected assay. Will
38
-be saved to \code{\link[SummarizedExperiment]{assay}}. Default
38
+be saved to \code{\link{assay}}. Default
39 39
 \code{"SCANORAMA"}.}
40 40
 }
41 41
 \value{
... ...
@@ -22,11 +22,11 @@ runSCMerge(
22 22
 batch correction. Default \code{"logcounts"}.}
23 23
 
24 24
 \item{batch}{A single character indicating a field in
25
-\code{\link[SummarizedExperiment]{colData}} that annotates the batches.
25
+\code{\link{colData}} that annotates the batches.
26 26
 Default \code{"batch"}.}
27 27
 
28 28
 \item{assayName}{A single characeter. The name for the corrected assay. Will
29
-be saved to \code{\link[SummarizedExperiment]{assay}}. Default
29
+be saved to \code{\link{assay}}. Default
30 30
 \code{"scMerge"}.}
31 31
 
32 32
 \item{seg}{A vector of gene names or indices that specifies SEG (Stably
... ...
@@ -23,24 +23,24 @@ runScranSNN(
23 23
 object.}
24 24
 
25 25
 \item{useAssay}{A single \code{character}, specifying which
26
-\code{\link[SummarizedExperiment]{assay}} to perform the clustering algorithm
26
+\code{\link{assay}} to perform the clustering algorithm
27 27
 on. Default \code{NULL}.}
28 28
 
29 29
 \item{useReducedDim}{A single \code{character}, specifying which
30
-low-dimension representation (\code{\link[SingleCellExperiment]{reducedDim}})
30
+low-dimension representation (\code{\link{reducedDim}})
31 31
 to perform the clustering algorithm on. Default \code{NULL}.}
32 32
 
33 33
 \item{useAltExp}{A single \code{character}, specifying the assay which
34
-\code{\link[SingleCellExperiment]{altExp}} to perform the clustering
34
+\code{\link{altExp}} to perform the clustering
35 35
 algorithm on. Default \code{NULL}.}
36 36
 
37 37
 \item{altExpAssay}{A single \code{character}, specifying which
38
-\code{\link[SummarizedExperiment]{assay}} in the chosen
39
-\code{\link[SingleCellExperiment]{altExp}} to work on. Only used when
38
+\code{\link{assay}} in the chosen
39
+\code{\link{altExp}} to work on. Only used when
40 40
 \code{useAltExp} is set. Default \code{"counts"}.}
41 41
 
42 42
 \item{clusterName}{A single \code{character}, specifying the name to store
43
-the cluster label in \code{\link[SummarizedExperiment]{colData}}. Default
43
+the cluster label in \code{\link{colData}}. Default
44 44
 \code{"scranSNN_cluster"}.}
45 45
 
46 46
 \item{k}{An \code{integer}, the number of nearest neighbors used to construct
... ...
@@ -124,7 +124,7 @@ If default, it is set to 30. Default \code{NULL}.}
124 124
 \value{
125 125
 A \link[SingleCellExperiment]{SingleCellExperiment} object with
126 126
  \code{scrub_doublets} output appended to the
127
- \link[SummarizedExperiment]{colData} slot. The columns include
127
+ \link{colData} slot. The columns include
128 128
  \emph{scrublet_score} and \emph{scrublet_call}.
129 129
 }
130 130
 \description{
... ...
@@ -23,7 +23,7 @@ batch correction. Note that ZINBWaVE works for counts (integer) input rather
23 23
 than logcounts that other methods prefer. Default \code{"counts"}.}
24 24
 
25 25
 \item{batch}{A single character indicating a field in
26
-\code{\link[SummarizedExperiment]{colData}} that annotates the batches.
26
+\code{\link{colData}} that annotates the batches.
27 27
 Default \code{"batch"}.}
28 28
 
29 29
 \item{nHVG}{An integer. Number of highly variable genes to use when fitting
... ...
@@ -8,8 +8,7 @@ sampleSummaryStats(inSCE, sample = NULL, useAssay = "counts", simple = TRUE)
8 8
 }
9 9
 \arguments{
10 10
 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object with saved
11
-\link[SummarizedExperiment]{assay} data and/or
12
-\link[SummarizedExperiment]{colData} data. Required.}
11
+\link{assay} data and/or \link{colData} data. Required.}
13 12
 
14 13
 \item{sample}{Character vector. Indicates which sample each cell belongs to.}
15 14
 
... ...
@@ -3,7 +3,7 @@
3 3
 \name{scater_logNormCounts}
4 4
 \alias{scater_logNormCounts}
5 5
 \title{scater_logNormCounts
6
-Uses \link[scater]{logNormCounts} to log normalize input data}
6
+Uses \link{logNormCounts} to log normalize input data}
7 7
 \usage{
8 8
 scater_logNormCounts(
9 9
   inSCE,
... ...
@@ -23,7 +23,7 @@ inSCE Updated SingleCellExperiment object that contains the new log normalized d
23 23
 }
24 24
 \description{
25 25
 scater_logNormCounts
26
-Uses \link[scater]{logNormCounts} to log normalize input data
26
+Uses \link{logNormCounts} to log normalize input data
27 27
 }
28 28
 \examples{
29 29
 data(sce_chcl, package = "scds")
... ...
@@ -33,16 +33,16 @@ sctkPythonInstallConda(
33 33
 The FALSE option is useful for situations where you don't want a pip install to attempt an overwrite of a conda binary package (e.g. SciPy on Windows which is very difficult
34 34
 to install via pip due to compilation requirements).}
35 35
 
36
-\item{pythonVersion}{Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL.}
36
+\item{pythonVersion}{Passed to \code{python_version} variable in \code{\link{conda_install}}. Default NULL.}
37 37
 
38
-\item{...}{Other parameters to pass to \code{\link[reticulate]{conda_install}}.}
38
+\item{...}{Other parameters to pass to \code{\link{conda_install}}.}
39 39
 }
40 40
 \value{
41 41
 None. Installation of Conda environment.
42 42
 }
43 43
 \description{
44 44
 Install all Python packages used in the \code{\link{singleCellTK}} package
45
-using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This
45
+using \code{\link{conda_install}} from package \code{\link{reticulate}}. This
46 46
 will create a new Conda environment with the name \code{envname} if not already present.
47 47
 Note that Anaconda or Miniconda already need to be installed on the local system.
48 48
 }
... ...
@@ -52,8 +52,8 @@ sctkPythonInstallConda(envname = "sctk-reticulate")
52 52
 }
53 53
 }
54 54
 \seealso{
55
-See \code{\link[reticulate]{conda_create}} for more information on creating a Conda environment.
56
-See \code{\link[reticulate]{conda_install}} for more description of the installation parameters.
55
+See \code{\link{conda_create}} for more information on creating a Conda environment.
56
+See \code{\link{conda_install}} for more description of the installation parameters.
57 57
 See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
58 58
 See \code{\link[singleCellTK]{selectSCTKConda}} for reloading the Conda environment if R is restarted without
59 59
 going through the whole installation process again.
... ...
@@ -26,7 +26,7 @@ None. Installation of virtual environment.
26 26
 }
27 27
 \description{
28 28
 Install all Python packages used in the \code{\link{singleCellTK}} package
29
-using \code{\link[reticulate]{virtualenv_install}} from package \code{\link{reticulate}}. This
29
+using \code{\link{virtualenv_install}} from package \code{\link{reticulate}}. This
30 30
 will create a new virtual environment with the name \code{envname} if not already present.
31 31
 }
32 32
 \examples{
... ...
@@ -35,8 +35,8 @@ sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")
35 35
 }
36 36
 }
37 37
 \seealso{
38
-See \code{\link[reticulate]{virtualenv_create}} for more information on creating a Conda environment.
39
-See \code{\link[reticulate]{virtualenv_install}} for more description of the installation parameters.
38
+See \code{\link{virtualenv_create}} for more information on creating a Conda environment.
39
+See \code{\link{virtualenv_install}} for more description of the installation parameters.
40 40
 See \url{https://rstudio.github.io/reticulate/} for more information on package \code{\link{reticulate}}.
41 41
 See \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} for reloading the virtual environment if R is restarted without
42 42
 going through the whole installation process again.
... ...
@@ -60,7 +60,7 @@ indicate the correct rows to keep. The various methods,
60 60
 with one another. If \code{returnAsAltExp} is set to \code{TRUE},
61 61
 then the returned object will have the same number of rows as the input
62 62
 \code{inSCE} as the subsetted object will be stored in the
63
-\code{\link[SingleCellExperiment]{altExp}} slot.
63
+\code{\link{altExp}} slot.
64 64
 }
65 65
 \examples{
66 66
 data(scExample)