now normalizeSparaseEset returnes eset with dgCMatrix

jyyulab · Aug 14, 2024 · 3a77678 · 3a77678
1 parent 0685034
commit 3a77678
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Showing 2 changed files with 23 additions and 5 deletions.
diff --git a/R/manipulate_sparseEset.R b/R/manipulate_sparseEset.R
@@ -4,6 +4,7 @@
 #' @title SparseExpressionSet
 #' @exportClass SparseExpressionSet
 #' @import Biobase
+#'
 methods::setClass(Class = "SparseExpressionSet",
                   contains = "ExpressionSet",
                   prototype = methods::prototype(methods::new("VersionedBiobase", versions = c(Biobase::classVersion("ExpressionSet"), SparseExpressionSet = "1.0.0" )))
@@ -35,9 +36,20 @@ methods::setClass(Class = "SparseExpressionSet",
 #'
 #' @examples
 #' data("pbmc14k_rawCount")
+#' ## 1. Create SparseEset object solely from raw count matrix
 #' pbmc14k_raw.eset <- createSparseEset(input_matrix = pbmc14k_rawCount,
 #'                                      projectID = "PBMC14k",
 #'                                      addMetaData = TRUE)
+#'
+#' ## 2. Create SparseEset with customized meta data
+#' true_label <- read.table(system.file("extdata/demo_pbmc14k/PBMC14k_trueLabel.txt.gz", package = "scMINER"),
+#'                          header = T, row.names = 1, sep = "\t", quote = "", stringsAsFactors = FALSE)
+#' pbmc14k_raw.eset <- createSparseEset(input_matrix = pbmc14k_rawCount,
+#'                                      cellData = true_label,
+#'                                      featureData = NULL,
+#'                                      projectID = "PBMC14k",
+#'                                      addMetaData = TRUE)
+#'
 createSparseEset <- function(input_matrix,
                              do.sparseConversion = TRUE,
                              cellData = NULL,
@@ -155,6 +167,7 @@ createSparseEset <- function(input_matrix,
 #'                                    addSurfix = NULL,
 #'                                    addMetaData = TRUE,
 #'                                    imputeNA = TRUE)
+#'
 combineSparseEset <- function(eset_list,
                               projectID = NULL,
                               addPrefix = NULL,
@@ -285,13 +298,11 @@ combineSparseEset <- function(eset_list,
 #' @export
 #'
 #' @examples
-#' true_label <- read.table(system.file("extdata/demo_pbmc14k/PBMC14k_trueLabel.txt.gz", package = "scMINER"),
-#'                          header = T, row.names = 1, sep = "\t", quote = "", stringsAsFactors = FALSE)
-#' pbmc14k_raw.eset <- createSparseEset(input_matrix = pbmc14k_rawCount,
-#'                                      cellData = true_label,
-#'                                      featureData = NULL,
+#' data("pbmc14k_expression.eset")
+#' pbmc14k_raw.eset <- updateSparseEset(input_eset = pbmc14k_expression.eset,
 #'                                      projectID = "PBMC14k",
 #'                                      addMetaData = TRUE)
+#'
 updateSparseEset <- function(input_eset,
                              dataMatrix = NULL,
                              cellData = NULL,

diff --git a/R/read_input.R b/R/read_input.R
@@ -30,6 +30,7 @@
 #'                                   featureType = "gene_symbol",
 #'                                   removeSuffix = TRUE,
 #'                                   addPrefix = "demoSample")
+#'
 readInput_10x.dir <- function(input_dir,
                               featureType = "gene_symbol",
                               removeSuffix = TRUE, addPrefix = NULL)
@@ -145,6 +146,7 @@ readInput_10x.dir <- function(input_dir,
 #'                                  featureType = "gene_symbol",
 #'                                  removeSuffix = TRUE,
 #'                                  addPrefix = "demoSample")
+#'
 readInput_10x.h5 <- function(h5_file,
                              featureType = "gene_symbol",
                              removeSuffix = TRUE,
@@ -252,6 +254,7 @@ readInput_10x.h5 <- function(h5_file,
 #' sparseMatrix <- readInput_h5ad(h5ad_file,
 #'                                removeSuffix = FALSE,
 #'                                addPrefix = "demoSample")
+#'
 readInput_h5ad <- function(h5ad_file,
                            removeSuffix = FALSE, addPrefix = NULL)
 {
@@ -322,6 +325,7 @@ readInput_h5ad <- function(h5ad_file,
 #'                                 is.geneBYcell = TRUE,
 #'                                 removeSuffix = FALSE,
 #'                                 addPrefix = "demoSample")
+#'
 readInput_table <- function(table_file, sep = "\t", is.geneBYcell = TRUE,
                             removeSuffix = FALSE, addPrefix = NULL)
 {
@@ -378,8 +382,11 @@ readInput_table <- function(table_file, sep = "\t", is.geneBYcell = TRUE,
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' scminer_dir <- createProjectSpace(project_dir = "path-to-a-folder",
 #'                                   project_name = "PBMC14k")
+#' }
+#'
 createProjectSpace <- function(project_dir,
                                project_name,
                                do.unlink = FALSE)