restruct se0 object

nshen7 · Nov 22, 2023 · 37ae2df · 37ae2df
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diff --git a/R/HDF5NAdrop2matrix.R b/R/HDF5NAdrop2matrix.R
@@ -1,4 +1,4 @@
-#' Coerce a NA-dropped HDF5Matrix back to matrix form
+#' Coerce a NA-dropped HDF5Matrix back to regular matrix form where NAs are not dropped to 0.
 #'
 #' @param HDF5Matrix an HDF5Matrix (e.g. assay output from vmrseq::data.pool)
 #' with dropped NA values

diff --git a/data/se0.rda b/data/se0.rda
diff --git a/data/se0/assays.h5 b/data/se0/assays.h5
diff --git a/data/se0/se.rds b/data/se0/se.rds
diff --git a/vignettes/vmrseq-vignette.Rmd b/vignettes/vmrseq-vignette.Rmd
@@ -71,14 +71,14 @@ head(cell_1)
 
 The `SummarizedExperiment` object stores CpG sites as rows and cells as columns. We adopted the NA-dropped sparseMatrix representation to save storage space for large single-cell datasets (see following section for specifics of how this representation look like). This option can be turned off but we recommend to keep it on. 
 
-Further, `data.pool` write the `SummarizedExperiment` object into disk using `HDF5` format, which is a backend extension of `DelayedArray`. The HDF5/DelayedArray format allows one to perform common array operations on it without loading the object in memory. See packages [HDF5Array](https://bioconductor.org/packages/release/bioc/html/HDF5Array.html) and [DelayedArray](https://bioconductor.org/packages/release/bioc/html/DelayedArray.html) for details.
+Further, `data.pool` saves the `SummarizedExperiment` object into disk using `HDF5` format, which is a backend extension of `DelayedArray`. Using `HDF5::loadHDF5SummarizedExperiment()` to load saved HDF5SummarizedExperiment objects into R. The HDF5/DelayedArray format allows one to perform common array operations on it without loading the object in memory. See packages [HDF5Array](https://bioconductor.org/packages/release/bioc/html/HDF5Array.html) and [DelayedArray](https://bioconductor.org/packages/release/bioc/html/DelayedArray.html) for details.
 
 
 ## Load example data
 
 In this vignette, we use a formatted example dataset built in the package called `se0` that's ready to be input to model fitting function: 
 ```{r}
-data(se0)
+se0 <- loadHDF5SummarizedExperiment(system.file('data/se0', package = 'vmrseq'))
 ```
 
 It is a `SummarizedExperiment` object with one `assay` slot called `M_mat` that contains the binary methylation values of individual cells at CpG sites (sites as rows and cells as columns):