... | ... |
@@ -10,7 +10,7 @@ |
10 | 10 |
# Patch delayed decorator. |
11 | 11 |
if (! is.null({pretty_patched = attr(decorator, 'calls')})) |
12 | 12 |
pretty_decorators = c(pretty_patched, pretty_decorators[-1]) |
13 |
- |
|
13 |
+ |
|
14 | 14 |
# Handle operator precedence so that we can chain decorators. |
15 | 15 |
if (inherits(f, 'decorator')) |
16 | 16 |
.delayed_decorate(decorator, f, pretty_decorators) |
... | ... |
@@ -29,7 +29,7 @@ print.decorated = function (x, useSource = TRUE, ...) { |
29 | 29 |
attr(bare, 'decorators') = NULL |
30 | 30 |
bare |
31 | 31 |
} |
32 |
- |
|
32 |
+ |
|
33 | 33 |
fun_def = utils::capture.output(print.function(bare(x), useSource = useSource, ...)) |
34 | 34 |
for (decorator in attr(x, 'decorators')) |
35 | 35 |
cat(deparse(decorator), '%@%\n') |
... | ... |
@@ -54,11 +54,12 @@ pretty_code = function (f) { |
54 | 54 |
.delayed_decorate = function (d1, d2, decorator_calls) |
55 | 55 |
structure(decorator(function (f) d1(d2(f))), calls = decorator_calls) |
56 | 56 |
|
57 |
-#' |
|
57 |
+#' |
|
58 | 58 |
#' @name simpleLog |
59 | 59 |
#' @title A decorator that prints the arguments to the decorated function |
60 | 60 |
#' @param f A function to decorate |
61 |
-#' |
|
61 |
+#' @return Prints message |
|
62 |
+#' |
|
62 | 63 |
simpleLog <- decorator %@% function(f) { |
63 | 64 |
function(...) { |
64 | 65 |
message(deparse(match.call())) |
... | ... |
@@ -18,6 +18,7 @@ |
18 | 18 |
#' @param compressionOpts Integer. Sets the compression level |
19 | 19 |
#' @param forceDense Default \code{False} Write sparse data as a dense matrix. |
20 | 20 |
#' Refer \code{anndata.write_h5ad} documentation for details. Default \code{NULL}. |
21 |
+#' @return Generates a Python anndata object containing data from \code{inSCE}. |
|
21 | 22 |
#' @examples |
22 | 23 |
#' data(sce_chcl, package = "scds") |
23 | 24 |
#' exportSCEtoAnnData(sce=sce_chcl, compression="gzip") |
... | ... |
@@ -11,6 +11,7 @@ |
11 | 11 |
#' gzip compressed. \code{FALSE} otherwise. Default |
12 | 12 |
#' \code{TRUE}. |
13 | 13 |
#' @param sample Name of the sample. It will be used as the prefix of file names. |
14 |
+#' @return Generates text files containing data from \code{inSCE}. |
|
14 | 15 |
#' @examples |
15 | 16 |
#' data(sce_chcl, package = "scds") |
16 | 17 |
#' exportSCEtoFlatFile(sce_chcl, "sce_chcl") |
... | ... |
@@ -37,6 +37,7 @@ |
37 | 37 |
#' 68,579 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.} |
38 | 38 |
#' } |
39 | 39 |
#' @author Joshua D. Campbell, David Jenkins |
40 |
+#' @return The specified \link[SingleCellExperiment]{SingleCellExperiment} object. |
|
40 | 41 |
#' @examples |
41 | 42 |
#' sce <- importExampleData("pbmc3k") |
42 | 43 |
#' @export |
... | ... |
@@ -35,6 +35,9 @@ |
35 | 35 |
#' \link{importGeneSetsFromCollection} for importing from |
36 | 36 |
#' \linkS4class{GeneSetCollection} objects, and |
37 | 37 |
#' \link{importGeneSetsFromMSigDB} for importing MSigDB gene sets. |
38 |
+#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object |
|
39 |
+#' with gene set from \code{collectionName} output stored to the |
|
40 |
+#' \link[SummarizedExperiment]{metadata} slot. |
|
38 | 41 |
#' @examples |
39 | 42 |
#' data(scExample) |
40 | 43 |
#' |
... | ... |
@@ -87,6 +90,9 @@ importGeneSetsFromGMT <- function(inSCE, file, |
87 | 90 |
#' can point to different locations within \code{inSCE}. See |
88 | 91 |
#' \link{featureIndex} for more information. |
89 | 92 |
#' Default \code{"rownames"}. |
93 |
+#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object |
|
94 |
+#' with gene set from \code{collectionName} output stored to the |
|
95 |
+#' \link[SummarizedExperiment]{metadata} slot. |
|
90 | 96 |
#' @details The gene identifiers in gene sets in \code{geneSetList} will be |
91 | 97 |
#' mapped to the rownames of \code{inSCE} using the \code{by} parameter and |
92 | 98 |
#' stored in a \linkS4class{GeneSetCollection} object from package |
... | ... |
@@ -182,6 +188,9 @@ importGeneSetsFromList <- function(inSCE, geneSetList, |
182 | 188 |
#' in the \code{GeneSetCollection}. |
183 | 189 |
#' See \link{featureIndex} for more information. |
184 | 190 |
#' Default \code{"rownames"}. |
191 |
+#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object |
|
192 |
+#' with gene set from \code{collectionName} output stored to the |
|
193 |
+#' \link[SummarizedExperiment]{metadata} slot. |
|
185 | 194 |
#' @details The gene identifiers in gene sets in the |
186 | 195 |
#' \code{GeneSetCollection} will be mapped to the rownames of |
187 | 196 |
#' \code{inSCE} using the \code{by} parameter and |
... | ... |
@@ -304,6 +313,9 @@ importGeneSetsFromCollection <- function(inSCE, geneSetCollection, |
304 | 313 |
#' of \code{inSCE}. See \link{featureIndex} for more information. |
305 | 314 |
#' Default \code{"rownames"}. |
306 | 315 |
#' @param verbose Boolean. Whether to display progress. Default \code{TRUE}. |
316 |
+#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object |
|
317 |
+#' with gene set from \code{collectionName} output stored to the |
|
318 |
+#' \link[SummarizedExperiment]{metadata} slot. |
|
307 | 319 |
#' @details The gene identifiers in gene sets from MSigDB will be retrieved |
308 | 320 |
#' using the \code{\link{msigdbr}} package. They will be mapped to the IDs in |
309 | 321 |
#' \code{inSCE} using the \code{by} parameter and |
... | ... |
@@ -420,6 +432,7 @@ importGeneSetsFromMSigDB <- function(inSCE, categoryIDs, |
420 | 432 |
#' @description Returns a vector of GeneSetCollections that have been |
421 | 433 |
#' imported and stored in \code{metadata(inSCE)$sctk$genesets}. |
422 | 434 |
#' @param inSCE A \link[SingleCellExperiment]{SingleCellExperiment} object. |
435 |
+#' @return Character vector. |
|
423 | 436 |
#' @author Joshua D. Campbell |
424 | 437 |
#' @seealso \link{importGeneSetsFromList} for importing from lists, |
425 | 438 |
#' \link{importGeneSetsFromGMT} for importing from GMT files, |
... | ... |
@@ -456,6 +469,7 @@ sctkListGeneSetCollections <- function(inSCE) { |
456 | 469 |
#' @description Returns a data.frame that shows MSigDB categories and |
457 | 470 |
#' subcategories as well as descriptions for each. The entries in the ID |
458 | 471 |
#' column in this table can be used as input for \link{importGeneSetsFromMSigDB}. |
472 |
+#' @return data.frame, containing MSigDB categories |
|
459 | 473 |
#' @author Joshua D. Campbell |
460 | 474 |
#' @seealso \link{importGeneSetsFromMSigDB} for importing MSigDB gene sets. |
461 | 475 |
#' @export |
... | ... |
@@ -6,6 +6,7 @@ |
6 | 6 |
#' used when running a differential expression analysis function. |
7 | 7 |
#' @param labelBy A single character for a column of \code{rowData(inSCE)} as |
8 | 8 |
#' where to search for the labeling text. Default \code{NULL}. |
9 |
+#' @return Stop point if found |
|
9 | 10 |
.checkDiffExpResultExists <- function(inSCE, useResult, labelBy = NULL){ |
10 | 11 |
if(!inherits(inSCE, 'SingleCellExperiment')){ |
11 | 12 |
stop('Given object is not a valid SingleCellExperiment object.') |
... | ... |
@@ -43,6 +43,7 @@ |
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 | 47 |
#' @examples |
47 | 48 |
#' mat <- readSingleCellMatrix(system.file("extdata/hgmm_1k_v3_20x20/outs/", |
48 | 49 |
#' "filtered_feature_bc_matrix/matrix.mtx.gz", package = "singleCellTK")) |
... | ... |
@@ -44,6 +44,7 @@ ad <- NULL |
44 | 44 |
#' to install via pip due to compilation requirements). |
45 | 45 |
#' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL. |
46 | 46 |
#' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}. |
47 |
+#' @return None. Installation of Conda environment. |
|
47 | 48 |
#' @examples |
48 | 49 |
#' \dontrun{ |
49 | 50 |
#' sctkPythonInstallConda(envname = "sctk-reticulate") |
... | ... |
@@ -93,6 +94,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate", |
93 | 94 |
#' @param packages Character Vector. List of packages to install. |
94 | 95 |
#' @param selectEnvironment Boolean. Run \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} after installing all packages to select the virtual environment. Default TRUE. |
95 | 96 |
#' @param python The path to a Python interpreter, to be used with the created virtual environment. When NULL, the Python interpreter associated with the current session will be used. Default NULL. |
97 |
+#' @return None. Installation of virtual environment. |
|
96 | 98 |
#' @examples |
97 | 99 |
#' \dontrun{ |
98 | 100 |
#' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate") |
... | ... |
@@ -124,6 +126,7 @@ sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate", |
124 | 126 |
#' @title Selects a Conda environment |
125 | 127 |
#' @description Selects a Conda environment with Python packages used in \code{\link{singleCellTK}}. |
126 | 128 |
#' @param envname Character. Name of the conda environment to activate. |
129 |
+#' @return None. Selects Conda environment. |
|
127 | 130 |
#' @examples |
128 | 131 |
#' \dontrun{ |
129 | 132 |
#' sctkPythonInstallConda(envname = "sctk-reticulate", selectConda = FALSE) |
... | ... |
@@ -157,6 +160,7 @@ selectSCTKConda <- function(envname = "sctk-reticulate") { |
157 | 160 |
#' @title Selects a virtual environment |
158 | 161 |
#' @description Selects a virtual environment with Python packages used in \code{\link{singleCellTK}} |
159 | 162 |
#' @param envname Character. Name of the virtual environment to activate. |
163 |
+#' @return None. Selects virtual environment. |
|
160 | 164 |
#' @examples |
161 | 165 |
#' \dontrun{ |
162 | 166 |
#' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate", selectEnvironment = FALSE) |
... | ... |
@@ -106,16 +106,19 @@ |
106 | 106 |
return(df) |
107 | 107 |
} |
108 | 108 |
|
109 |
-#' @title Plot table of SCTK QC outputs. |
|
110 |
-#' @description Plot QC metrics generated from QC algorithms via either kable or csv file. |
|
109 |
+#' @title Generate table of SCTK QC outputs. |
|
110 |
+#' @description Creates a table of QC metrics generated from |
|
111 |
+#' QC algorithms via either kable or csv file. |
|
111 | 112 |
#' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved |
112 |
-#' dimension reduction components or a variable with saved results. Required |
|
113 |
+#' \link[SummarizedExperiment]{assay} data and/or |
|
114 |
+#' \link[SummarizedExperiment]{colData} data. Required. |
|
113 | 115 |
#' @param sample Character vector. Indicates which sample each cell belongs to. |
114 | 116 |
#' @param useAssay A string specifying which assay in the SCE to use. Default |
115 | 117 |
#' 'counts'. |
116 | 118 |
#' @param simple Boolean. Indicates whether to generate a table of only |
117 | 119 |
#' basic QC stats (ex. library size), or to generate a summary table of all |
118 | 120 |
#' QC stats stored in the inSCE. |
121 |
+#' @return A matrix/array object. |
|
119 | 122 |
#' @examples |
120 | 123 |
#' data(scExample, package = "singleCellTK") |
121 | 124 |
#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") |
... | ... |
@@ -9,6 +9,7 @@ |
9 | 9 |
#' @param directory Output directory. Default is './'. |
10 | 10 |
#' @param format The format of output. It currently supports flat files, rds files |
11 | 11 |
#' and python h5 files. It can output multiple formats. Default: c("SCE", "AnnData", "FlatFile", "HTAN"). |
12 |
+#' @return Generates a file containing data from \code{inSCE} as \code{format}. |
|
12 | 13 |
#' @examples |
13 | 14 |
#' exportSCE(mouseBrainSubsetSCE, format = "SCE") |
14 | 15 |
#' @export |
... | ... |
@@ -190,6 +191,7 @@ generateMeta <- function(dropletSCE = NULL, |
190 | 191 |
#' @param samplename The sample name of the \link[SingleCellExperiment]{SingleCellExperiment} objects. |
191 | 192 |
#' @param writeYAML Whether output yaml file to store parameters. Default if TRUE. If FALSE, |
192 | 193 |
#' return character object. |
194 |
+#' @return If \code{writeYAML} TRUE, a yaml object will be generated. If FALSE, character object. |
|
193 | 195 |
#' @export |
194 | 196 |
getSceParams <- function(inSCE, |
195 | 197 |
skip = c("scrublet", "runDecontX","runBarcodeRanksMetaOutput"), |
... | ... |
@@ -493,6 +493,8 @@ seuratHeatmapPlot <- function(plotObject, dims, ncol, labels) { |
493 | 493 |
#' @param assaySlotSCE Selected assay to update in the input SingleCellExperiment object |
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 |
+#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with |
|
497 |
+#' data from Seurat object appended to the \link[SummarizedExperiment]{assay} slot. |
|
496 | 498 |
#' @importFrom SummarizedExperiment assay<- |
497 | 499 |
.updateAssaySCE <- function(inSCE, seuratObject, assaySlotSCE, seuratDataSlot = "counts", seuratAssaySlot = "RNA") { |
498 | 500 |
assay(inSCE, assaySlotSCE) <- NULL |
... | ... |
@@ -17,6 +17,9 @@ used when running a differential expression analysis function.} |
17 | 17 |
\item{labelBy}{A single character for a column of \code{rowData(inSCE)} as |
18 | 18 |
where to search for the labeling text. Default \code{NULL}.} |
19 | 19 |
} |
20 |
+\value{ |
|
21 |
+Stop point if found |
|
22 |
+} |
|
20 | 23 |
\description{ |
21 | 24 |
Check if the specified MAST result in SingleCellExperiment object is |
22 | 25 |
complete. But does not garantee the biological correctness. |
... | ... |
@@ -24,6 +24,10 @@ Update/Modify/Add an assay in the provided SingleCellExperiment object from a Se |
24 | 24 |
|
25 | 25 |
\item{seuratAssaySlot}{Selected assay from Seurat object. Default \code{"RNA"}.} |
26 | 26 |
} |
27 |
+\value{ |
|
28 |
+A \link[SingleCellExperiment]{SingleCellExperiment} object with |
|
29 |
+ data from Seurat object appended to the \link[SummarizedExperiment]{assay} slot. |
|
30 |
+} |
|
27 | 31 |
\description{ |
28 | 32 |
.updateAssaySCE |
29 | 33 |
Update/Modify/Add an assay in the provided SingleCellExperiment object from a Seurat object |
... | ... |
@@ -28,6 +28,9 @@ It can be 'Droplets'(raw droplets matrix) or 'Cells' (cells matrix).} |
28 | 28 |
\item{format}{The format of output. It currently supports flat files, rds files |
29 | 29 |
and python h5 files. It can output multiple formats. Default: c("SCE", "AnnData", "FlatFile", "HTAN").} |
30 | 30 |
} |
31 |
+\value{ |
|
32 |
+Generates a file containing data from \code{inSCE} as \code{format}. |
|
33 |
+} |
|
31 | 34 |
\description{ |
32 | 35 |
Export data in SingleCellExperiment object |
33 | 36 |
} |
... | ... |
@@ -38,6 +38,9 @@ Default \code{"counts"}.} |
38 | 38 |
\item{forceDense}{Default \code{False} Write sparse data as a dense matrix. |
39 | 39 |
Refer \code{anndata.write_h5ad} documentation for details. Default \code{NULL}.} |
40 | 40 |
} |
41 |
+\value{ |
|
42 |
+Generates a Python anndata object containing data from \code{inSCE}. |
|
43 |
+} |
|
41 | 44 |
\description{ |
42 | 45 |
Writes all assays, colData, rowData, reducedDims, and altExps objects in a |
43 | 46 |
\link[SingleCellExperiment]{SingleCellExperiment} to a Python annData object in the .h5ad format |
... | ... |
@@ -27,6 +27,9 @@ gzip compressed. \code{FALSE} otherwise. Default |
27 | 27 |
|
28 | 28 |
\item{sample}{Name of the sample. It will be used as the prefix of file names.} |
29 | 29 |
} |
30 |
+\value{ |
|
31 |
+Generates text files containing data from \code{inSCE}. |
|
32 |
+} |
|
30 | 33 |
\description{ |
31 | 34 |
Writes all assays, colData, rowData, reducedDims, and altExps objects in a |
32 | 35 |
\link[SingleCellExperiment]{SingleCellExperiment} to text files. |
... | ... |
@@ -28,6 +28,9 @@ getSceParams( |
28 | 28 |
\item{writeYAML}{Whether output yaml file to store parameters. Default if TRUE. If FALSE, |
29 | 29 |
return character object.} |
30 | 30 |
} |
31 |
+\value{ |
|
32 |
+If \code{writeYAML} TRUE, a yaml object will be generated. If FALSE, character object. |
|
33 |
+} |
|
31 | 34 |
\description{ |
32 | 35 |
Extract QC parameters from the SingleCellExperiment object |
33 | 36 |
} |
... | ... |
@@ -18,6 +18,9 @@ will store the data as a sparse matrix from package \link{Matrix} while |
18 | 18 |
\item{delayedArray}{Boolean. Whether to read the expression matrix as |
19 | 19 |
\link[DelayedArray]{DelayedArray} object or not. Default \code{FALSE}.} |
20 | 20 |
} |
21 |
+\value{ |
|
22 |
+The specified \link[SingleCellExperiment]{SingleCellExperiment} object. |
|
23 |
+} |
|
21 | 24 |
\description{ |
22 | 25 |
Retrieves published example datasets stored in |
23 | 26 |
\link[SingleCellExperiment]{SingleCellExperiment} using the |
... | ... |
@@ -37,6 +37,11 @@ in the \code{GeneSetCollection}. |
37 | 37 |
See \link{featureIndex} for more information. |
38 | 38 |
Default \code{"rownames"}.} |
39 | 39 |
} |
40 |
+\value{ |
|
41 |
+A \link[SingleCellExperiment]{SingleCellExperiment} object |
|
42 |
+with gene set from \code{collectionName} output stored to the |
|
43 |
+\link[SummarizedExperiment]{metadata} slot. |
|
44 |
+} |
|
40 | 45 |
\description{ |
41 | 46 |
Converts a list of gene sets stored in a |
42 | 47 |
\linkS4class{GeneSetCollection} object and stores it in the metadata of the |
... | ... |
@@ -39,6 +39,11 @@ Default \code{"rownames"}.} |
39 | 39 |
|
40 | 40 |
\item{sep}{Character. Delimiter of the GMT file. Default \code{"\t"}.} |
41 | 41 |
} |
42 |
+\value{ |
|
43 |
+A \link[SingleCellExperiment]{SingleCellExperiment} object |
|
44 |
+ with gene set from \code{collectionName} output stored to the |
|
45 |
+ \link[SummarizedExperiment]{metadata} slot. |
|
46 |
+} |
|
42 | 47 |
\description{ |
43 | 48 |
Converts a list of gene sets stored in a GMT file into a |
44 | 49 |
\linkS4class{GeneSetCollection} and stores it in the metadata of the |
... | ... |
@@ -36,6 +36,11 @@ can point to different locations within \code{inSCE}. See |
36 | 36 |
\link{featureIndex} for more information. |
37 | 37 |
Default \code{"rownames"}.} |
38 | 38 |
} |
39 |
+\value{ |
|
40 |
+A \link[SingleCellExperiment]{SingleCellExperiment} object |
|
41 |
+with gene set from \code{collectionName} output stored to the |
|
42 |
+\link[SummarizedExperiment]{metadata} slot. |
|
43 |
+} |
|
39 | 44 |
\description{ |
40 | 45 |
Converts a list of gene sets into a |
41 | 46 |
\linkS4class{GeneSetCollection} and stores it in the metadata of the |
... | ... |
@@ -39,6 +39,11 @@ Default \code{"rownames"}.} |
39 | 39 |
|
40 | 40 |
\item{verbose}{Boolean. Whether to display progress. Default \code{TRUE}.} |
41 | 41 |
} |
42 |
+\value{ |
|
43 |
+A \link[SingleCellExperiment]{SingleCellExperiment} object |
|
44 |
+with gene set from \code{collectionName} output stored to the |
|
45 |
+\link[SummarizedExperiment]{metadata} slot. |
|
46 |
+} |
|
42 | 47 |
\description{ |
43 | 48 |
Gets a list of MSigDB gene sets stores it in the metadata of the |
44 | 49 |
\linkS4class{SingleCellExperiment} object. These gene sets can be used in |
... | ... |
@@ -33,6 +33,9 @@ Default \code{NULL}.} |
33 | 33 |
feature (gene) index .npy file. Used only if \code{file} has .npz extension. |
34 | 34 |
Default \code{NULL}.} |
35 | 35 |
} |
36 |
+\value{ |
|
37 |
+A \link[DelayedArray]{DelayedArray} object or matrix. |
|
38 |
+} |
|
36 | 39 |
\description{ |
37 | 40 |
Automatically detact the format of the input file and read |
38 | 41 |
the file. |
... | ... |
@@ -2,13 +2,14 @@ |
2 | 2 |
% Please edit documentation in R/sampleSummaryStats.R |
3 | 3 |
\name{sampleSummaryStats} |
4 | 4 |
\alias{sampleSummaryStats} |
5 |
-\title{Plot table of SCTK QC outputs.} |
|
5 |
+\title{Generate table of SCTK QC outputs.} |
|
6 | 6 |
\usage{ |
7 | 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 |
-dimension reduction components or a variable with saved results. Required} |
|
11 |
+\link[SummarizedExperiment]{assay} data and/or |
|
12 |
+\link[SummarizedExperiment]{colData} data. Required.} |
|
12 | 13 |
|
13 | 14 |
\item{sample}{Character vector. Indicates which sample each cell belongs to.} |
14 | 15 |
|
... | ... |
@@ -19,8 +20,12 @@ dimension reduction components or a variable with saved results. Required} |
19 | 20 |
basic QC stats (ex. library size), or to generate a summary table of all |
20 | 21 |
QC stats stored in the inSCE.} |
21 | 22 |
} |
23 |
+\value{ |
|
24 |
+A matrix/array object. |
|
25 |
+} |
|
22 | 26 |
\description{ |
23 |
-Plot QC metrics generated from QC algorithms via either kable or csv file. |
|
27 |
+Creates a table of QC metrics generated from |
|
28 |
+ QC algorithms via either kable or csv file. |
|
24 | 29 |
} |
25 | 30 |
\examples{ |
26 | 31 |
data(scExample, package = "singleCellTK") |
... | ... |
@@ -9,6 +9,9 @@ sctkListGeneSetCollections(inSCE) |
9 | 9 |
\arguments{ |
10 | 10 |
\item{inSCE}{A \link[SingleCellExperiment]{SingleCellExperiment} object.} |
11 | 11 |
} |
12 |
+\value{ |
|
13 |
+Character vector. |
|
14 |
+} |
|
12 | 15 |
\description{ |
13 | 16 |
Returns a vector of GeneSetCollections that have been |
14 | 17 |
imported and stored in \code{metadata(inSCE)$sctk$genesets}. |
... | ... |
@@ -37,6 +37,9 @@ to install via pip due to compilation requirements).} |
37 | 37 |
|
38 | 38 |
\item{...}{Other parameters to pass to \code{\link[reticulate]{conda_install}}.} |
39 | 39 |
} |
40 |
+\value{ |
|
41 |
+None. Installation of Conda environment. |
|
42 |
+} |
|
40 | 43 |
\description{ |
41 | 44 |
Install all Python packages used in the \code{\link{singleCellTK}} package |
42 | 45 |
using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This |
... | ... |
@@ -21,6 +21,9 @@ sctkPythonInstallVirtualEnv( |
21 | 21 |
|
22 | 22 |
\item{python}{The path to a Python interpreter, to be used with the created virtual environment. When NULL, the Python interpreter associated with the current session will be used. Default NULL.} |
23 | 23 |
} |
24 |
+\value{ |
|
25 |
+None. Installation of virtual environment. |
|
26 |
+} |
|
24 | 27 |
\description{ |
25 | 28 |
Install all Python packages used in the \code{\link{singleCellTK}} package |
26 | 29 |
using \code{\link[reticulate]{virtualenv_install}} from package \code{\link{reticulate}}. This |
... | ... |
@@ -9,6 +9,9 @@ selectSCTKConda(envname = "sctk-reticulate") |
9 | 9 |
\arguments{ |
10 | 10 |
\item{envname}{Character. Name of the conda environment to activate.} |
11 | 11 |
} |
12 |
+\value{ |
|
13 |
+None. Selects Conda environment. |
|
14 |
+} |
|
12 | 15 |
\description{ |
13 | 16 |
Selects a Conda environment with Python packages used in \code{\link{singleCellTK}}. |
14 | 17 |
} |
... | ... |
@@ -9,6 +9,9 @@ selectSCTKVirtualEnvironment(envname = "sctk-reticulate") |
9 | 9 |
\arguments{ |
10 | 10 |
\item{envname}{Character. Name of the virtual environment to activate.} |
11 | 11 |
} |
12 |
+\value{ |
|
13 |
+None. Selects virtual environment. |
|
14 |
+} |
|
12 | 15 |
\description{ |
13 | 16 |
Selects a virtual environment with Python packages used in \code{\link{singleCellTK}} |
14 | 17 |
} |
... | ... |
@@ -25,10 +25,14 @@ then \code{"x < 5"} will return all columns with x less than 5. |
25 | 25 |
Single quotes should be used for character strings. For example, |
26 | 26 |
\code{"y == 'yes'"} will return all columns where y is "yes". |
27 | 27 |
Multiple expressions can be evaluated by placing them in a vector. |
28 |
-For example \code{c("x < 5", "y =='yes'")} will apply both operations for |
|
28 |
+For example \code{c("x < 5", "y =='yes'")} will apply both operations for |
|
29 | 29 |
subsetting. If \code{NULL}, this will not be used for subsetting. |
30 | 30 |
Default \code{NULL}.} |
31 | 31 |
} |
32 |
+\value{ |
|
33 |
+A \link[SingleCellExperiment]{SingleCellExperiment} object that has |
|
34 |
+been subsetted by colData. |
|
35 |
+} |
|
32 | 36 |
\description{ |
33 | 37 |
Used to peform subsetting of a |
34 | 38 |
\linkS4class{SingleCellExperiment} object using a variety of methods that |
... | ... |
@@ -38,7 +42,7 @@ with one another. |
38 | 42 |
} |
39 | 43 |
\examples{ |
40 | 44 |
data(scExample) |
41 |
-sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") |
|
45 |
+sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") |
|
42 | 46 |
} |
43 | 47 |
\author{ |
44 | 48 |
Joshua D. Campbell |
... | ... |
@@ -29,14 +29,14 @@ for subsetting. Default \code{NULL}.} |
29 | 29 |
\item{rowData}{Character. An expression that will identify a subset of rows |
30 | 30 |
using variables found in the \code{rowData} of \code{inSCE}. For example, |
31 | 31 |
if \code{x} is a numeric vector in \code{rowData}, then \code{"x < 5"} will |
32 |
-return all rows with x less than 5. Single quotes should be used for |
|
32 |
+return all rows with x less than 5. Single quotes should be used for |
|
33 | 33 |
character strings. For example, \code{"y == 'yes'"} will return all |
34 | 34 |
rows where y is "yes". Multiple expressions can be evaluated by placing them |
35 | 35 |
in a vector. For example \code{c("x < 5", "y =='yes'")} will apply both |
36 | 36 |
operations for subsetting. If \code{NULL}, this will not be used for |
37 | 37 |
subsetting. Default \code{NULL}.} |
38 | 38 |
|
39 |
-\item{returnAsAltExp}{Boolean. If \code{TRUE}, the subsetted |
|
39 |
+\item{returnAsAltExp}{Boolean. If \code{TRUE}, the subsetted |
|
40 | 40 |
\linkS4class{SingleCellExperiment} object will be returned in the |
41 | 41 |
\code{altExp} slot of \code{inSCE}. If \code{FALSE}, the subsetted |
42 | 42 |
\linkS4class{SingleCellExperiment} object will be directly returned.} |
... | ... |
@@ -48,6 +48,10 @@ add if \code{returnAsAltExp = TRUE}. Default \code{subset}.} |
48 | 48 |
be added to the beginning of the assay names in the \code{altExp} object. |
49 | 49 |
This is only utilized if \code{returnAsAltExp = TRUE}. Default \code{TRUE}.} |
50 | 50 |
} |
51 |
+\value{ |
|
52 |
+A \link[SingleCellExperiment]{SingleCellExperiment} object that has |
|
53 |
+been subsetted by rowData. |
|
54 |
+} |
|
51 | 55 |
\description{ |
52 | 56 |
Used to peform subsetting of a |
53 | 57 |
\linkS4class{SingleCellExperiment} object using a variety of methods that |
... | ... |
@@ -64,7 +68,7 @@ data(scExample) |
64 | 68 |
# Set a variable up in the rowData indicating mitochondrial genes |
65 | 69 |
rowData(sce)$isMito <- ifelse(grepl("^MT-", rowData(sce)$feature_name), |
66 | 70 |
"yes", "no") |
67 |
-sce <- subsetSCERows(sce, rowData = "isMito == 'yes'") |
|
71 |
+sce <- subsetSCERows(sce, rowData = "isMito == 'yes'") |
|
68 | 72 |
} |
69 | 73 |
\author{ |
70 | 74 |
Joshua D. Campbell |