update docs

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 4.2.1.9000
+Version: 4.2.1.9001
 Date: 2022-11-09
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. 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>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

R/convenience.R

@@ -172,6 +172,10 @@ LoadVizgen <- function(data.dir, fov, assay = 'Vizgen', z = 3L) {
 
 #' @return \code{LoadXenium}: A \code{\link[SeuratObject]{Seurat}} object
 #'
+#' @param data.dir Path to folder containing Nanostring SMI outputs
+#' @param fov FOV name
+#' @param assay Assay name
+#'
 #' @importFrom SeuratObject Cells CreateCentroids CreateFOV
 #' CreateSegmentation CreateSeuratObject
 #'

R/preprocessing.R

@@ -8,7 +8,7 @@ NULL
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 globalVariables(
-  names = c('fov', 'cell_ID'),
+  names = c('fov', 'cell_ID', 'qv'),
   package = 'Seurat',
   add = TRUE
 )
@@ -1994,18 +1994,6 @@ ReadNanostring <- function(
 #' @param mols.qv.threshold Remove transcript molecules with
 #' a QV less than this threshold. QV >= 20 is the standard threshold
 #' used to construct the cell x gene count matrix.
-#' @param mols.filter Filter molecules that match provided string
-#' @param genes.filter Filter genes from cell x gene matrix that match
-#' provided string
-
-#' @param subset.counts.matrix If the counts matrix should be built from
-#' molecule coordinates for a specific segmentation; One of:
-#' \itemize{
-#'  \item \dQuote{Nuclear}: nuclear segmentations
-#'  \item \dQuote{Cytoplasm}: cell cytoplasm segmentations
-#'  \item \dQuote{Membrane}: cell membrane segmentations
-#' }
-#' @param cell.mols.only If TRUE, only load molecules within a cell
 #'
 #' @return \code{ReadXenium}: A list with some combination of the
 #' following values: