doc: Update count_mat docs (#73)

R/err.R

@@ -78,7 +78,7 @@ create_bugreport_from_seurat <- function(obj) {
 #' This bugreport can then be included when reaching out to 10xGenomics Support or when filing
 #' a Github ticket.  This information should be included along with any other output when creating a Loupe file.
 #'
-#' @param count_mat A sparse dgCMatrix
+#' @param count_mat A sparse dgCMatrix as is generated via Matrix::rsparsematrix.  Rows are features, Columns are barcodes.
 #' @param clusters list of factors that hold information for each barcode
 #' @param projections list of matrices, all with dimensions (barcodeCount x 2)
 #' @param assay_name optional string that holds the Seurat Object assay name.

R/hdf5.R

@@ -1,6 +1,6 @@
 #' Create an hdf5 interchange file
 #'
-#' @param count_mat A sparse dgCMatrix
+#' @param count_mat A sparse dgCMatrix as is generated via Matrix::rsparsematrix.  Rows are features, Columns are barcodes.
 #' @param clusters list of factors that hold information for each barcode
 #' @param projections list of matrices, all with dimensions (barcodeCount x 2)
 #' @param h5path path to h5 file
@@ -40,7 +40,7 @@ create_hdf5 <- function(
 #' Writes the matrix to the H5 file
 #'
 #' @param f An open H5File
-#' @param count_mat A sparse dgCMatrix
+#' @param count_mat A sparse dgCMatrix as is generated via Matrix::rsparsematrix.  Rows are features, Columns are barcodes.
 #' @param feature_ids optional character vector that specifies the feature ids of the count matrix.  Typically, these are the ensemble ids.
 #'
 #' @noRd

R/lib.R

@@ -75,7 +75,7 @@ create_loupe_from_seurat <- function(
 
 #' Create a Loupe file
 #'
-#' @param count_mat A sparse dgCMatrix
+#' @param count_mat A sparse dgCMatrix as is generated via Matrix::rsparsematrix.  Rows are features, Columns are barcodes.
 #' @param clusters list of factors that hold information for each barcode
 #' @param projections list of matrices, all with dimensions (barcodeCount x 2)
 #' @param output_dir optional directory where the Loupe file will be written

R/validate.R

@@ -1,6 +1,6 @@
 #' Validate the seurat count matrix
 #'
-#' @param count_mat A sparse dgCMatrix
+#' @param count_mat A sparse dgCMatrix as is generated via Matrix::rsparsematrix.  Rows are features, Columns are barcodes.
 #' @param feature_ids optional character vector that specifies the feature ids of the count matrix.  Typically, these are the ensemble ids.
 #'
 #' @return A list with two elements: