add saving to README and vignette

Author: stemangiola

README.Rmd

@@ -141,6 +141,30 @@ single_cell_counts =
 single_cell_counts
 ```
 
+## Save your `SingleCellExperiment`
+
+The returned `SingleCellExperiment` can be saved with two modalities, as `.rds` or as `HDF5`.
+
+### Saving as RDS (fast saving, slow reading)
+
+Saving as `.rds` has the advantage that is very fast, the `.rds` file occupies very little disk space as it only stored the links for the files in your ache.
+
+However it has the disadvantage that for big `SingleCellExperiment` objects, which merge a lot of HDF5 from your `get_SingleCellExperiment` the display and manipulation is going to be slow.
+
+```{r, eval=FALSE}
+single_cell_counts |> saveRDS("single_cell_counts.rds")
+```
+
+### Saving as HDF5 (slow saving, fast reading)
+
+Saving as `.rds` has the advantage that rewrites on disk a monolithic `HDF5` and so displaying and manipulating large `SingleCellExperiment` objects, which merge a lot of HDF5 from your `get_SingleCellExperiment`, is going to be fast.
+
+However it has the disadvantage that the files are going to be larger as they include the count information, and the saving process is going to be slow for large objects.
+
+```{r, eval=FALSE}
+single_cell_counts |> saveHDF5SummarizedExperiment("single_cell_counts")
+```
+
 ## Visualise gene transcription
 
 We can gather all CD14 monocytes cells and plot the distribution of HLA-A across all tissues
@@ -322,3 +346,4 @@ This project has been funded by
 - *Bioconductor core funding* NIH NHGRI 5U24HG004059-18 
 - *Victoria Cancer Agency* ECRF21036
 - *Australian National Health and Medical Research Council* 1116955
+- *The Lorenzo and Pamela Galli Medical Research Trust*

README.md

@@ -216,6 +216,40 @@ single_cell_counts
 #> Active assay: originalexp (35615 features, 0 variable features)
 ```
 
+## Save your `SingleCellExperiment`
+
+The returned `SingleCellExperiment` can be saved with two modalities, as
+`.rds` or as `HDF5`.
+
+### Saving as RDS (fast saving, slow reading)
+
+Saving as `.rds` has the advantage that is very fast, the `.rds` file
+occupies very little disk space as it only stored the links for the
+files in your ache.
+
+However it has the disadvantage that for big `SingleCellExperiment`
+objects, which merge a lot of HDF5 from your `get_SingleCellExperiment`
+the display and manipulation is going to be slow.
+
+``` r
+single_cell_counts |> saveRDS("single_cell_counts.rds")
+```
+
+### Saving as HDF5 (slow saving, fast reading)
+
+Saving as `.rds` has the advantage that rewrites on disk a monolithic
+`HDF5` and so displaying and manipulating large `SingleCellExperiment`
+objects, which merge a lot of HDF5 from your `get_SingleCellExperiment`,
+is going to be fast.
+
+However it has the disadvantage that the files are going to be larger as
+they include the count information, and the saving process is going to
+be slow for large objects.
+
+``` r
+single_cell_counts |> saveHDF5SummarizedExperiment("single_cell_counts")
+```
+
 ## Visualise gene transcription
 
 We can gather all CD14 monocytes cells and plot the distribution of
@@ -356,3 +390,4 @@ This project has been funded by
 - *Bioconductor core funding* NIH NHGRI 5U24HG004059-18
 - *Victoria Cancer Agency* ECRF21036
 - *Australian National Health and Medical Research Council* 1116955
+- *The Lorenzo and Pamela Galli Medical Research Trust*

vignettes/Introduction.Rmd

@@ -159,6 +159,30 @@ single_cell_counts =
 single_cell_counts
 ```
 
+## Save your `SingleCellExperiment`
+
+The returned `SingleCellExperiment` can be saved with two modalities, as `.rds` or as `HDF5`.
+
+### Saving as RDS (fast saving, slow reading)
+
+Saving as `.rds` has the advantage that is very fast, the `.rds` file occupies very little disk space as it only stored the links for the files in your ache.
+
+However it has the disadvantage that for big `SingleCellExperiment` objects, which merge a lot of HDF5 from your `get_SingleCellExperiment` the display and manipulation is going to be slow.
+
+```{r, eval=FALSE}
+single_cell_counts |> saveRDS("single_cell_counts.rds")
+```
+
+### Saving as HDF5 (slow saving, fast reading)
+
+Saving as `.rds` has the advantage that rewrites on disk a monolithic `HDF5` and so displaying and manipulating large `SingleCellExperiment` objects, which merge a lot of HDF5 from your `get_SingleCellExperiment`, is going to be fast.
+
+However it has the disadvantage that the files are going to be larger as they include the count information, and the saving process is going to be slow for large objects.
+
+```{r, eval=FALSE}
+single_cell_counts |> saveHDF5SummarizedExperiment("single_cell_counts")
+```
+
 ## Visualise gene transcription
 
 We can gather all CD14 monocytes cells and plot the distribution of HLA-A across all tissues