... | ... |
@@ -52,7 +52,7 @@ |
52 | 52 |
#' |
53 | 53 |
#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with |
54 | 54 |
#' 'decontX_Contamination' and 'decontX_Clusters' added to the |
55 |
-#' \link[SummarizedExperiment]{colData} slot. Additionally, the |
|
55 |
+#' \link{colData} slot. Additionally, the |
|
56 | 56 |
#' decontaminated counts will be added as an assay called 'decontXCounts'. |
57 | 57 |
#' @examples |
58 | 58 |
#' data(scExample, package = "singleCellTK") |
... | ... |
@@ -46,7 +46,7 @@ |
46 | 46 |
#' @param df See \link[DropletUtils]{emptyDrops} for more information. Default \code{20}. |
47 | 47 |
#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with the |
48 | 48 |
#' \link[DropletUtils]{barcodeRanks} output table appended to the |
49 |
-#' \link[SummarizedExperiment]{colData} slot. The columns include |
|
49 |
+#' \link{colData} slot. The columns include |
|
50 | 50 |
#' \emph{dropletUtils_BarcodeRank_Knee} and \emph{dropletUtils_BarcodeRank_Knee} |
51 | 51 |
#' Please refer to the documentation of \link[DropletUtils]{barcodeRanks} for |
52 | 52 |
#' details. |
... | ... |
@@ -45,7 +45,7 @@ |
45 | 45 |
#' @param BPPARAM See \link[DropletUtils]{emptyDrops} for more information. |
46 | 46 |
#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with the |
47 | 47 |
#' \link[DropletUtils]{emptyDrops} output table appended to the |
48 |
-#' \link[SummarizedExperiment]{colData} slot. The columns include |
|
48 |
+#' \link{colData} slot. The columns include |
|
49 | 49 |
#' \emph{emptyDrops_total}, \emph{emptyDrops_logprob}, |
50 | 50 |
#' \emph{emptyDrops_pvalue}, \emph{emptyDrops_limited}, \emph{emptyDrops_fdr}. |
51 | 51 |
#' Please refer to the documentation of \link[DropletUtils]{emptyDrops} for |
... | ... |
@@ -6,20 +6,20 @@ |
6 | 6 |
#' @param inSCE A \code{\link[SingleCellExperiment]{SingleCellExperiment}} |
7 | 7 |
#' object. |
8 | 8 |
#' @param useAssay A single \code{character}, specifying which |
9 |
-#' \code{\link[SummarizedExperiment]{assay}} to perform the clustering algorithm |
|
9 |
+#' \code{\link{assay}} to perform the clustering algorithm |
|
10 | 10 |
#' on. Default \code{NULL}. |
11 | 11 |
#' @param useReducedDim A single \code{character}, specifying which |
12 |
-#' low-dimension representation (\code{\link[SingleCellExperiment]{reducedDim}}) |
|
12 |
+#' low-dimension representation (\code{\link{reducedDim}}) |
|
13 | 13 |
#' to perform the clustering algorithm on. Default \code{NULL}. |
14 | 14 |
#' @param useAltExp A single \code{character}, specifying the assay which |
15 |
-#' \code{\link[SingleCellExperiment]{altExp}} to perform the clustering |
|
15 |
+#' \code{\link{altExp}} to perform the clustering |
|
16 | 16 |
#' algorithm on. Default \code{NULL}. |
17 | 17 |
#' @param altExpAssay A single \code{character}, specifying which |
18 |
-#' \code{\link[SummarizedExperiment]{assay}} in the chosen |
|
19 |
-#' \code{\link[SingleCellExperiment]{altExp}} to work on. Only used when |
|
18 |
+#' \code{\link{assay}} in the chosen |
|
19 |
+#' \code{\link{altExp}} to work on. Only used when |
|
20 | 20 |
#' \code{useAltExp} is set. Default \code{"counts"}. |
21 | 21 |
#' @param clusterName A single \code{character}, specifying the name to store |
22 |
-#' the cluster label in \code{\link[SummarizedExperiment]{colData}}. Default |
|
22 |
+#' the cluster label in \code{\link{colData}}. Default |
|
23 | 23 |
#' \code{"scranSNN_cluster"}. |
24 | 24 |
#' @param k An \code{integer}, the number of nearest neighbors used to construct |
25 | 25 |
#' the graph. Smaller value indicates higher resolution and larger number of |
... | ... |
@@ -109,7 +109,7 @@ runScranSNN <- function(inSCE, useAssay = NULL, useReducedDim = NULL, |
109 | 109 |
#' low-dimension representation to perform the clustering algorithm on. Default |
110 | 110 |
#' \code{"PCA"}. |
111 | 111 |
#' @param clusterName A single \code{character}, specifying the name to store |
112 |
-#' the cluster label in \code{\link[SummarizedExperiment]{colData}}. Default |
|
112 |
+#' the cluster label in \code{\link{colData}}. Default |
|
113 | 113 |
#' \code{"scranSNN_cluster"}. |
114 | 114 |
#' @param nCenters An \code{integer}, the number of centroids (clusters). |
115 | 115 |
#' @param nIter An \code{integer}, the maximum number of iterations allowed. |
... | ... |
@@ -9,11 +9,11 @@ |
9 | 9 |
#' selected.variable features. Default \code{NULL}. |
10 | 10 |
#' @param sample Character vector. Indicates which sample each cell belongs to. |
11 | 11 |
#' If given a single character, will take the annotation from |
12 |
-#' \code{\link[SummarizedExperiment]{colData}}. Default \code{NULL}. |
|
12 |
+#' \code{\link{colData}}. Default \code{NULL}. |
|
13 | 13 |
#' @param reducedDimName A name to store the results of the dimension reduction |
14 | 14 |
#' coordinates obtained from this method. Default \code{"UMAP"}. |
15 | 15 |
#' @param logNorm Whether the counts will need to be log-normalized prior to |
16 |
-#' generating the UMAP via \code{\link[scater]{logNormCounts}}. Default |
|
16 |
+#' generating the UMAP via \code{\link{logNormCounts}}. Default |
|
17 | 17 |
#' \code{TRUE}. |
18 | 18 |
#' @param nNeighbors The size of local neighborhood used for manifold |
19 | 19 |
#' approximation. Larger values result in more global views of the manifold, |
... | ... |
@@ -29,7 +29,7 @@ |
29 | 29 |
#' result on a more even dispersal of points. Default \code{0.01}. See |
30 | 30 |
#' `?uwot::umap` for more information. |
31 | 31 |
#' @param spread The effective scale of embedded points. In combination with |
32 |
-#' ‘min_dist’, this determines how clustered/clumped the embedded points are. |
|
32 |
+#' minDist, this determines how clustered/clumped the embedded points are. |
|
33 | 33 |
#' Default \code{1}. See `?uwot::umap` for more information. |
34 | 34 |
#' @param pca Logical. Whether to perform dimension reduction with PCA before |
35 | 35 |
#' UMAP. Default \code{TRUE} |
... | ... |
@@ -83,7 +83,7 @@ |
83 | 83 |
#' with the sample name appended to each colname in colData |
84 | 84 |
#' } |
85 | 85 |
#' @param delayedArray Boolean. Whether to read the expression matrix as |
86 |
-#' \link[DelayedArray]{DelayedArray} object. Default \code{TRUE}. |
|
86 |
+#' \link{DelayedArray} object. Default \code{TRUE}. |
|
87 | 87 |
#' @details |
88 | 88 |
#' \code{importAnnData} converts scRNA-seq data in the AnnData format to the |
89 | 89 |
#' \code{SingleCellExperiment} object. The .X slot in AnnData is transposed to the features x cells |
... | ... |
@@ -99,10 +99,10 @@ |
99 | 99 |
#' \code{samples}. |
100 | 100 |
#' @param class Character. The class of the expression matrix stored in the SCE |
101 | 101 |
#' object. Can be one of "Matrix" (as returned by |
102 |
-#' \link[Matrix]{readMM} function), or "matrix" (as returned by |
|
102 |
+#' \link{readMM} function), or "matrix" (as returned by |
|
103 | 103 |
#' \link[base]{matrix} function). Default "Matrix". |
104 | 104 |
#' @param delayedArray Boolean. Whether to read the expression matrix as |
105 |
-#' \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}. |
|
105 |
+#' \link[DelayedArray]{DelayedArray-class} object or not. Default \code{TRUE}. |
|
106 | 106 |
#' @return A \code{SingleCellExperiment} object containing the count |
107 | 107 |
#' matrix, the gene annotation, and the cell annotation. |
108 | 108 |
#' @examples |
... | ... |
@@ -433,7 +433,7 @@ |
433 | 433 |
#' \itemize{ |
434 | 434 |
#' \item \code{NULL}. All samples within \code{cellRangerDirs} will be |
435 | 435 |
#' imported. The order of samples will be first determined by the order of |
436 |
-#' \code{cellRangerDirs} and then by \link[base]{list.dirs}. This is only |
|
436 |
+#' \code{cellRangerDirs} and then by \link{list.dirs}. This is only |
|
437 | 437 |
#' for the case where \code{cellRangerDirs} is specified. |
438 | 438 |
#' \item A list of vectors containing the folder names for samples to import. |
439 | 439 |
#' Each vector in |
... | ... |
@@ -509,10 +509,10 @@ |
509 | 509 |
#' \code{unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE))}. |
510 | 510 |
#' @param class Character. The class of the expression matrix stored in the SCE |
511 | 511 |
#' object. Can be one of "Matrix" (as returned by |
512 |
-#' \link[Matrix]{readMM} function), or "matrix" (as returned by |
|
512 |
+#' \link{readMM} function), or "matrix" (as returned by |
|
513 | 513 |
#' \link[base]{matrix} function). Default \code{"Matrix"}. |
514 | 514 |
#' @param delayedArray Boolean. Whether to read the expression matrix as |
515 |
-#' \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}. |
|
515 |
+#' \link{DelayedArray} object or not. Default \code{TRUE}. |
|
516 | 516 |
#' @param reference Character vector. The reference genome names. |
517 | 517 |
#' Default \code{NULL}. If not \code{NULL}, it must gave the length and order as |
518 | 518 |
#' \code{length(unlist(sampleDirs))} if \code{sampleDirs} is not \code{NULL}. |
... | ... |
@@ -653,10 +653,10 @@ importCellRangerV2 <- function( |
653 | 653 |
#' Default "sample". |
654 | 654 |
#' @param class Character. The class of the expression matrix stored in the SCE |
655 | 655 |
#' object. Can be one of "Matrix" (as returned by |
656 |
-#' \link[Matrix]{readMM} function), or "matrix" (as returned by |
|
656 |
+#' \link{readMM} function), or "matrix" (as returned by |
|
657 | 657 |
#' \link[base]{matrix} function). Default "Matrix". |
658 | 658 |
#' @param delayedArray Boolean. Whether to read the expression matrix as |
659 |
-#' \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}. |
|
659 |
+#' \link{DelayedArray} object or not. Default \code{TRUE}. |
|
660 | 660 |
#' @return A \code{SingleCellExperiment} object containing the count |
661 | 661 |
#' matrix, the feature annotations, and the cell annotation for the sample. |
662 | 662 |
#' @examples |
... | ... |
@@ -737,10 +737,10 @@ importCellRangerV3 <- function( |
737 | 737 |
#' Default "sample". |
738 | 738 |
#' @param class Character. The class of the expression matrix stored in the SCE |
739 | 739 |
#' object. Can be one of "Matrix" (as returned by |
740 |
-#' \link[Matrix]{readMM} function), or "matrix" (as returned by |
|
740 |
+#' \link{readMM} function), or "matrix" (as returned by |
|
741 | 741 |
#' \link[base]{matrix} function). Default "Matrix". |
742 | 742 |
#' @param delayedArray Boolean. Whether to read the expression matrix as |
743 |
-#' \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}. |
|
743 |
+#' \link{DelayedArray} object or not. Default \code{TRUE}. |
|
744 | 744 |
#' @return A \code{SingleCellExperiment} object containing the count |
745 | 745 |
#' matrix, the feature annotations, and the cell annotation for the sample. |
746 | 746 |
#' @examples |
... | ... |
@@ -91,7 +91,7 @@ |
91 | 91 |
#' @param dataType can be "filtered" or "raw". Default \code{"filtered"}. |
92 | 92 |
#' @param rdsFileName File name prefix of the DropEst RDS output. default is "cell.counts" |
93 | 93 |
#' @param delayedArray Boolean. Whether to read the expression matrix as |
94 |
-#' \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}. |
|
94 |
+#' \link{DelayedArray} object or not. Default \code{TRUE}. |
|
95 | 95 |
#' @details |
96 | 96 |
#' \code{importDropEst} expects either raw counts matrix stored as "cm_raw" or filtered |
97 | 97 |
#' counts matrix stored as "cm" in the DropEst rds output. |
... | ... |
@@ -2,7 +2,7 @@ |
2 | 2 |
#' @title Retrieve example datasets |
3 | 3 |
#' @description Retrieves published example datasets stored in |
4 | 4 |
#' \link[SingleCellExperiment]{SingleCellExperiment} using the |
5 |
-#' \link[scRNAseq]{scRNAseq} and |
|
5 |
+#' \link{scRNAseq} and |
|
6 | 6 |
#' \link[TENxPBMCData]{TENxPBMCData} packages. See 'Details' for a |
7 | 7 |
#' list of available datasets. |
8 | 8 |
#' @param dataset Character. Name of the dataset to retrieve. |
... | ... |
@@ -12,16 +12,16 @@ |
12 | 12 |
#' \code{"matrix"} will store the data in a standard matrix. Default |
13 | 13 |
#' \code{"Matrix"}. |
14 | 14 |
#' @param delayedArray Boolean. Whether to read the expression matrix as |
15 |
-#' \link[DelayedArray]{DelayedArray} object or not. Default \code{FALSE}. |
|
15 |
+#' \link{DelayedArray} object or not. Default \code{FALSE}. |
|
16 | 16 |
#' @details See the list below for the available datasets and their |
17 | 17 |
#' descriptions. |
18 | 18 |
#' \describe{ |
19 | 19 |
#' \item{"fluidigm_pollen"}{Retrieved with |
20 |
-#' \code{\link[scRNAseq]{ReprocessedFluidigmData}}. Returns a dataset of 65 |
|
20 |
+#' \code{\link{ReprocessedFluidigmData}}. Returns a dataset of 65 |
|
21 | 21 |
#' human neural cells from Pollen et al. (2014), each sequenced at high and low |
22 | 22 |
#' coverage (SRA accession SRP041736).} |
23 | 23 |
#' \item{"allen_tasic"}{Retrieved with |
24 |
-#' \code{\link[scRNAseq]{ReprocessedAllenData}}. Returns a dataset of 379 mouse |
|
24 |
+#' \code{\link{ReprocessedAllenData}}. Returns a dataset of 379 mouse |
|
25 | 25 |
#' brain cells from Tasic et al. (2016).} |
26 | 26 |
#' \item{"pbmc3k"}{Retrieved with \code{\link[TENxPBMCData]{TENxPBMCData}}. |
27 | 27 |
#' 2,700 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.} |
... | ... |
@@ -31,7 +31,7 @@ |
31 | 31 |
#' frames instead of file paths. The default is FALSE. |
32 | 32 |
#' @param class Character. The class of the expression matrix stored in the SCE |
33 | 33 |
#' object. Can be one of "Matrix" (as returned by |
34 |
-#' \link[Matrix]{readMM} function), or "matrix" (as returned by |
|
34 |
+#' \link{readMM} function), or "matrix" (as returned by |
|
35 | 35 |
#' \link[base]{matrix} function). Default "Matrix". |
36 | 36 |
#' @param annotFileHeader Whether there's a header (colnames) in the cell annotation file. Default is FALSE |
37 | 37 |
#' @param annotFileRowName Which column is used as the rownames for the cell annotation file. Default is 1 (first column). |
... | ... |
@@ -41,7 +41,7 @@ |
41 | 41 |
#' @param featureSep Separater used for the feature annotation file. Default is "\\t". |
42 | 42 |
#' @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. |
43 | 43 |
#' @param 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 |
#' @return a SingleCellExperiment object |
46 | 46 |
#' @export |
47 | 47 |
|
... | ... |
@@ -4,7 +4,7 @@ |
4 | 4 |
#' \linkS4class{SingleCellExperiment} object. These gene sets can be used in |
5 | 5 |
#' downstream quality control and analysis functions in \link{singleCellTK}. |
6 | 6 |
#' @param inSCE Input \linkS4class{SingleCellExperiment} object. |
7 |
-#' @param file Character. Path to GMT file. See \link[GSEABase]{getGmt} for |
|
7 |
+#' @param file Character. Path to GMT file. See \link{getGmt} for |
|
8 | 8 |
#' more information on reading GMT files. |
9 | 9 |
#' @param collectionName Character. Name of collection to add gene sets to. |
10 | 10 |
#' If this collection already exists in \code{inSCE}, then these gene sets will |
... | ... |
@@ -37,7 +37,7 @@ |
37 | 37 |
#' \link{importGeneSetsFromMSigDB} for importing MSigDB gene sets. |
38 | 38 |
#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object |
39 | 39 |
#' with gene set from \code{collectionName} output stored to the |
40 |
-#' \link[S4Vectors]{metadata} slot. |
|
40 |
+#' \link{metadata} slot. |
|
41 | 41 |
#' @examples |
42 | 42 |
#' data(scExample) |
43 | 43 |
#' |
... | ... |
@@ -92,7 +92,7 @@ importGeneSetsFromGMT <- function(inSCE, file, |
92 | 92 |
#' Default \code{"rownames"}. |
93 | 93 |
#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object |
94 | 94 |
#' with gene set from \code{collectionName} output stored to the |
95 |
-#' \link[S4Vectors]{metadata} slot. |
|
95 |
+#' \link{metadata} slot. |
|
96 | 96 |
#' @details The gene identifiers in gene sets in \code{geneSetList} will be |
97 | 97 |
#' mapped to the rownames of \code{inSCE} using the \code{by} parameter and |
98 | 98 |
#' stored in a \linkS4class{GeneSetCollection} object from package |
... | ... |
@@ -169,7 +169,7 @@ importGeneSetsFromList <- function(inSCE, geneSetList, |
169 | 169 |
#' downstream quality control and analysis functions in \link{singleCellTK}. |
170 | 170 |
#' @param inSCE Input \linkS4class{SingleCellExperiment} object. |
171 | 171 |
#' @param geneSetCollection A \linkS4class{GeneSetCollection} object. See |
172 |
-#' \link[GSEABase]{GeneSetCollection} for more details. |
|
172 |
+#' \link{GeneSetCollection} for more details. |
|
173 | 173 |
#' @param collectionName Character. Name of collection to add gene sets to. |
174 | 174 |
#' If this collection already exists in \code{inSCE}, then these gene sets will |
175 | 175 |
#' be added to that collection. Any gene sets within the collection with the |
... | ... |
@@ -190,7 +190,7 @@ importGeneSetsFromList <- function(inSCE, geneSetList, |
190 | 190 |
#' Default \code{"rownames"}. |
191 | 191 |
#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object |
192 | 192 |
#' with gene set from \code{collectionName} output stored to the |
193 |
-#' \link[S4Vectors]{metadata} slot. |
|
193 |
+#' \link{metadata} slot. |
|
194 | 194 |
#' @details The gene identifiers in gene sets in the |
195 | 195 |
#' \code{GeneSetCollection} will be mapped to the rownames of |
196 | 196 |
#' \code{inSCE} using the \code{by} parameter and |
... | ... |
@@ -315,7 +315,7 @@ importGeneSetsFromCollection <- function(inSCE, geneSetCollection, |
315 | 315 |
#' @param verbose Boolean. Whether to display progress. Default \code{TRUE}. |
316 | 316 |
#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object |
317 | 317 |
#' with gene set from \code{collectionName} output stored to the |
318 |
-#' \link[S4Vectors]{metadata} slot. |
|
318 |
+#' \link{metadata} slot. |
|
319 | 319 |
#' @details The gene identifiers in gene sets from MSigDB will be retrieved |
320 | 320 |
#' using the \code{\link{msigdbr}} package. They will be mapped to the IDs in |
321 | 321 |
#' \code{inSCE} using the \code{by} parameter and |
... | ... |
@@ -2,7 +2,7 @@ |
2 | 2 |
#' Imports samples from different sources and compiles them into a list of SCE objects |
3 | 3 |
#' @param allImportEntries object containing the sources and parameters of all the samples being imported (from the UI) |
4 | 4 |
#' @param delayedArray Boolean. Whether to read the expression matrix as |
5 |
-#' \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}. |
|
5 |
+#' \link{DelayedArray} object or not. Default \code{TRUE}. |
|
6 | 6 |
#' @return A list of \link[SingleCellExperiment]{SingleCellExperiment} object containing |
7 | 7 |
#' the droplet or cell data or both,depending on the dataType that users provided. |
8 | 8 |
#' @export |
... | ... |
@@ -243,10 +243,10 @@ |
243 | 243 |
#' optimus_v1.4.0. |
244 | 244 |
#' @param class Character. The class of the expression matrix stored in the SCE |
245 | 245 |
#' object. Can be one of "Matrix" (as returned by |
246 |
-#' \link[Matrix]{readMM} function), or "matrix" (as returned by |
|
246 |
+#' \link{readMM} function), or "matrix" (as returned by |
|
247 | 247 |
#' \link[base]{matrix} function). Default "Matrix". |
248 | 248 |
#' @param delayedArray Boolean. Whether to read the expression matrix as |
249 |
-#' \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}. |
|
249 |
+#' \link{DelayedArray} object or not. Default \code{TRUE}. |
|
250 | 250 |
#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object |
251 | 251 |
#' containing the count |
252 | 252 |
#' matrix, the gene annotation, and the cell annotation. |
... | ... |
@@ -107,10 +107,10 @@ |
107 | 107 |
#' length as \code{samples}. |
108 | 108 |
#' @param class Character. The class of the expression matrix stored in the SCE |
109 | 109 |
#' object. Can be one of "Matrix" (as returned by |
110 |
-#' \link[Matrix]{readMM} function), or "matrix" (as returned by |
|
110 |
+#' \link{readMM} function), or "matrix" (as returned by |
|
111 | 111 |
#' \link[base]{matrix} function). Default "Matrix". |
112 | 112 |
#' @param delayedArray Boolean. Whether to read the expression matrix as |
113 |
-#' \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}. |
|
113 |
+#' \link{DelayedArray} object or not. Default \code{TRUE}. |
|
114 | 114 |
#' @return A \code{SingleCellExperiment} object containing the count |
115 | 115 |
#' matrix, the gene annotation, and the cell annotation. |
116 | 116 |
#' @examples |
... | ... |
@@ -164,10 +164,10 @@ |
164 | 164 |
#' Default \code{FALSE}. |
165 | 165 |
#' @param class Character. The class of the expression matrix stored in the SCE |
166 | 166 |
#' object. Can be one of "Matrix" (as returned by |
167 |
-#' \link[Matrix]{readMM} function), or "matrix" (as returned by |
|
167 |
+#' \link{readMM} function), or "matrix" (as returned by |
|
168 | 168 |
#' \link[base]{matrix} function). Default "Matrix". |
169 | 169 |
#' @param delayedArray Boolean. Whether to read the expression matrix as |
170 |
-#' \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}. |
|
170 |
+#' \link{DelayedArray} object or not. Default \code{TRUE}. |
|
171 | 171 |
#' @param feNotFirstCol Boolean. \code{TRUE} if first column of |
172 | 172 |
#' sparse_counts_genes.csv |
173 | 173 |
#' is row index and it will be removed. \code{FALSE} the first column will |
... | ... |
@@ -40,7 +40,7 @@ |
40 | 40 |
#' @param axis Choose from \code{"col"} or \code{"row"}. |
41 | 41 |
#' @param colorGen A function that generates color code vector by giving an |
42 | 42 |
#' integer for the number of colors. Alternatively, |
43 |
-#' \code{\link[grDevices]{rainbow}}. Default \code{\link{distinctColors}}. |
|
43 |
+#' \code{\link{rainbow}}. Default \code{\link{distinctColors}}. |
|
44 | 44 |
#' @return A \code{list} object containing distinct colors mapped to all |
45 | 45 |
#' possible categorical entries in \code{rowData(inSCE)} or |
46 | 46 |
#' \code{colData(inSCE)}. |
... | ... |
@@ -36,14 +36,14 @@ |
36 | 36 |
#' will convert to a sparse format which should be used |
37 | 37 |
#' for datasets with large numbers of cells. Default "Matrix". |
38 | 38 |
#' @param delayedArray Boolean. Whether to read the expression matrix as |
39 |
-#' \link[DelayedArray]{DelayedArray} object or not. Default \code{TRUE}. |
|
39 |
+#' \link{DelayedArray} object or not. Default \code{TRUE}. |
|
40 | 40 |
#' @param colIndexLocation Character. For Optimus output, the path to the |
41 | 41 |
#' barcode index .npy file. Used only if \code{file} has .npz extension. |
42 | 42 |
#' Default \code{NULL}. |
43 | 43 |
#' @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. |
45 | 45 |
#' Default \code{NULL}. |
46 |
-#' @return A \link[DelayedArray]{DelayedArray} object or matrix. |
|
46 |
+#' @return A \link{DelayedArray} object or matrix. |
|
47 | 47 |
#' @examples |
48 | 48 |
#' mat <- readSingleCellMatrix(system.file("extdata/hgmm_1k_v3_20x20/outs/", |
49 | 49 |
#' "filtered_feature_bc_matrix/matrix.mtx.gz", package = "singleCellTK")) |
... | ... |
@@ -30,7 +30,7 @@ ad <- NULL |
30 | 30 |
#' @name sctkPythonInstallConda |
31 | 31 |
#' @title Installs Python packages into a Conda environment |
32 | 32 |
#' @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 |
|
33 |
+#' using \code{\link{conda_install}} from package \code{\link{reticulate}}. This |
|
34 | 34 |
#' will create a new Conda environment with the name \code{envname} if not already present. |
35 | 35 |
#' Note that Anaconda or Miniconda already need to be installed on the local system. |
36 | 36 |
#' @param envname Character. Name of the conda environment to create. |
... | ... |
@@ -42,15 +42,15 @@ ad <- NULL |
42 | 42 |
#' @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. |
43 | 43 |
#' 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 |
44 | 44 |
#' to install via pip due to compilation requirements). |
45 |
-#' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL. |
|
46 |
-#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}. |
|
45 |
+#' @param pythonVersion Passed to \code{python_version} variable in \code{\link{conda_install}}. Default NULL. |
|
46 |
+#' @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 |
} |
... | ... |
@@ -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) |