CRAN release

.Rbuildignore

@@ -15,4 +15,7 @@
 ^.*\.h5Seurat$
 ^.*\.rds$
 ^.*\.Rds$
+^LICENSE$
 ^data-raw$
+^inst$
+^tests$

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: SeuratObject
 Type: Package
 Title: Data Structures for Single Cell Data
-Version: 0.0.0.9000
-Date: 2020-08-10
+Version: 4.0.0
+Date: 2021-01-07
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Andrew', family = 'Butler', email = 'abutler@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),
@@ -17,12 +17,16 @@ Authors@R: c(
 Description: Defines S4 classes for single-cell genomic data and associated
   information, such as dimensionality reduction embeddings, nearest-neighbor
   graphs, and spatially-resolved coordinates. Provides data access methods and
-  R-native hooks to ensure the Seurat object is familiar to other R users.
-URL: http://www.satijalab.org/seurat,
+  R-native hooks to ensure the Seurat object is familiar to other R users. See 
+  Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, 
+  Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, 
+  and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for 
+  more details.
+URL: https://satijalab.org/seurat,
       https://github.com/mojaveazure/seurat-object
 BugReports:
       https://github.com/mojaveazure/seurat-object/issues
-License: GPL-3 | file LICENSE
+License: GPL-3
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.1

R/assay.R

@@ -68,6 +68,8 @@ Assay <- setClass(
 #' @param min.features Include cells where at least this many features are
 #' detected.
 #'
+#' @return A \code{\link{Assay}} object
+#'
 #' @importFrom methods as
 #' @importFrom Matrix colSums rowSums
 #'
@@ -1173,6 +1175,8 @@ setMethod(
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \donttest{
 #' calcn <- SeuratObject:::CalcN(pbmc_small[["RNA"]])
@@ -1197,6 +1201,8 @@ CalcN <- function(object) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 IsSCT <- function(assay) {
   if (is.list(x = assay)) {
     sct.check <- lapply(X = assay, FUN = function(x) {
@@ -1215,6 +1221,8 @@ IsSCT <- function(assay) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 SubsetVST <- function(sct.info, cells, features) {
   cells.keep <- intersect(x = cells, y = rownames(x = sct.info$cell_attr))
   sct.info$cell_attr <- sct.info$cell_attr[cells.keep, ]
@@ -1241,6 +1249,8 @@ SubsetVST <- function(sct.info, cells, features) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 ValidateDataForMerge <- function(assay, slot) {
   mat <- GetAssayData(object = assay, slot = slot)
   if (any(dim(x = mat) == c(0, 0))) {

R/dimreduc.R

@@ -66,6 +66,8 @@ DimReduc <- setClass(
 #' @param misc list for the user to store any additional information associated
 #' with the dimensional reduction
 #'
+#' @return A \code{\link{DimReduc}} object
+#'
 #' @aliases SetDimReduction
 #'
 #' @export
@@ -777,6 +779,8 @@ setMethod(
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 Projected <- function(object) {
   return(!IsMatrixEmpty(x = Loadings(object = object, projected = TRUE)))
 }

R/generics.R

@@ -10,7 +10,9 @@ NULL
 #' variance). To add cell level information, add to the Seurat object. If adding
 #' feature-level metadata, add to the Assay object (e.g. \code{object[["RNA"]]})
 #'
-#' @inheritParams .AddMetaData
+#' @param object An object
+#' @param metadata A vector, list, or data.frame with metadata to add
+#' @param col.name A name for meta data if not a named list or data.frame
 #'
 #' @return \code{object} with metadata added
 #'
@@ -79,6 +81,8 @@ as.Neighbor <- function(x, ...) {
 #' @param x An object to convert to class \code{Seurat}
 #' @param ... Arguments passed to other methods
 #'
+#' @return A \code{\link{Seurat}} object generated from \code{x}
+#'
 #' @rdname as.Seurat
 #' @export as.Seurat
 #'
@@ -218,6 +222,8 @@ DefaultAssay <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
+#' @return The distance matrix
+#'
 #' @rdname Distances
 #' @export Distances
 #'
@@ -232,6 +238,8 @@ Distances <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
+#' @return The embeddings matrix
+#'
 #' @rdname Embeddings
 #' @export Embeddings
 #'
@@ -475,6 +483,9 @@ IsGlobal <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
+#' @return \code{JS}: either a \code{\link{JackStrawData}} object or the
+#' specified jackstraw data
+#'
 #' @rdname JS
 #' @export JS
 #'
@@ -486,6 +497,8 @@ JS <- function(object, ...) {
 
 #' @param value JackStraw information
 #'
+#' @return \code{JS<-}: \code{object} with the update jackstraw information
+#'
 #' @rdname JS
 #' @export JS<-
 #'
@@ -498,6 +511,8 @@ JS <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
+#' @return \code{Key}: the object key
+#'
 #' @rdname Key
 #' @export Key
 #'
@@ -509,6 +524,8 @@ Key <- function(object, ...) {
 
 #' @param value Key value
 #'
+#' @return \code{Key<-}: \code{object} with an updated key
+#'
 #' @rdname Key
 #' @export Key<-
 #'
@@ -523,6 +540,8 @@ Key <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
+#' @return \code{Loadings}: the feature loadings for \code{object}
+#'
 #' @rdname Loadings
 #' @export Loadings
 #'
@@ -534,6 +553,8 @@ Loadings <- function(object, ...) {
 
 #' @param value Feature loadings to add
 #'
+#' @return \code{Loadings<-}: \code{object} with the updated loadings
+#'
 #' @rdname Loadings
 #' @export Loadings<-
 #'
@@ -724,6 +745,8 @@ StashIdent <- function(object, save.name, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
+#' @return The standard deviations
+#'
 #' @rdname Stdev
 #' @export Stdev
 #'

R/seurat.R

@@ -2990,6 +2990,8 @@ setMethod(
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \donttest{
 #' SeuratObject:::Collections(pbmc_small)
@@ -3022,6 +3024,8 @@ Collections <- function(object) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 DefaultImage <- function(object) {
   object <- UpdateSlots(object = object)
   images <- Images(object = object, assay = DefaultAssay(object = object))
@@ -3041,6 +3045,8 @@ DefaultImage <- function(object) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 FilterObjects <- function(object, classes.keep = c('Assay', 'DimReduc')) {
   object <- UpdateSlots(object = object)
   slots <- na.omit(object = Filter(
@@ -3080,6 +3086,8 @@ FilterObjects <- function(object, classes.keep = c('Assay', 'DimReduc')) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \donttest{
 #' SeuratObject:::FindObject(pbmc_small, name = "RNA")
@@ -3133,6 +3141,8 @@ FindObject <- function(object, name) {
 #'
 #' @seealso \code{\link[sctransform]{get_residuals}}
 #'
+#' @noRd
+#'
 #' @examples
 #' \dontrun{
 #' pbmc_small <- SCTransform(pbmc_small, variable.features.n = 20)
@@ -3377,6 +3387,8 @@ GetResidualVstOut <- function(
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 UpdateAssay <- function(old.assay, assay) {
   cells <- colnames(x = old.assay@data)
   counts <- old.assay@raw.data
@@ -3405,7 +3417,7 @@ UpdateAssay <- function(old.assay, assay) {
 #'
 #' @rdname V2Update
 #'
-#' @keywords internal
+#' @noRd
 #'
 UpdateDimReduction <- function(old.dr, assay) {
   new.dr <- list()
@@ -3453,6 +3465,8 @@ UpdateDimReduction <- function(old.dr, assay) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 UpdateJackstraw <- function(old.jackstraw) {
   if (is.null(x = old.jackstraw)) {
     new.jackstraw <- new(

R/spatial.R

@@ -374,6 +374,8 @@ setMethod(
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 NullImage <- function(mode = c('grob', 'raster', 'plotly', 'raw')) {
   mode <- mode[1]
   mode <- match.arg(arg = mode)

R/utils.R

@@ -321,6 +321,8 @@ S4ToList.list <- function(object) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 CheckDots <- function(..., fxns = NULL) {
   args.names <- names(x = list(...))
   if (length(x = list(...)) == 0) {
@@ -460,6 +462,8 @@ CheckDots <- function(..., fxns = NULL) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 CheckDuplicateCellNames <- function(object.list, verbose = TRUE, stop = FALSE) {
   cell.names <- unlist(x = lapply(X = object.list, FUN = colnames))
   if (any(duplicated(x = cell.names))) {
@@ -497,6 +501,8 @@ CheckDuplicateCellNames <- function(object.list, verbose = TRUE, stop = FALSE) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \donttest{
 #' SeuratObject:::ExtractField('Hello World', field = 1, delim = '_')
@@ -526,6 +532,8 @@ ExtractField <- function(string, field = 1, delim = "_") {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \donttest{
 #' SeuratObject:::IsMatrixEmpty(new("matrix"))
@@ -553,6 +561,8 @@ IsMatrixEmpty <- function(x) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 IsNullPtr <- function(x) {
   stopifnot(is(object = x, class2 = 'externalptr'))
   return(.Call('isnull', x))
@@ -572,6 +582,8 @@ IsNullPtr <- function(x) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 #' @examples
 #' \dontrun{
 #' set.seed(42L)
@@ -608,6 +620,8 @@ RandomName <- function(length = 5L, ...) {
 #'
 #' @seealso \code{\link{s4list}}
 #'
+#' @noRd
+#'
 SwapClassPkg <- function(x, from = NULL, to = NULL) {
   if (!inherits(x = x, what = 'list')) {
     return(x)
@@ -659,6 +673,8 @@ SwapClassPkg <- function(x, from = NULL, to = NULL) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 Top <- function(data, num = 20, balanced = FALSE) {
   nr <- nrow(x = data)
   if (num > nr) {
@@ -699,6 +715,8 @@ Top <- function(data, num = 20, balanced = FALSE) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 UpdateClassPkg <- function(object, from = NULL, to = NULL) {
   if (!isS4(object)) {
     return(object)
@@ -719,6 +737,8 @@ UpdateClassPkg <- function(object, from = NULL, to = NULL) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 UpdateSlots <- function(object) {
   object.list <- sapply(
     X = slotNames(x = object),
@@ -759,6 +779,8 @@ UpdateSlots <- function(object) {
 #'
 #' @keywords internal
 #'
+#' @noRd
+#'
 UpdateKey <- function(key) {
   if (grepl(pattern = '^[[:alnum:]]+_$', x = key)) {
     return(key)