Updated vignette to use listDatasets.

Removed unnecessary 10X commentary.
melanieloth · Jun 7, 2020 · 1d1d237 · 1d1d237
1 parent 2410cfe
commit 1d1d237
Showing 1 changed file with 28 additions and 53 deletions.
diff --git a/vignettes/scRNAseq.Rmd b/vignettes/scRNAseq.Rmd
@@ -39,54 +39,34 @@ for further information on how to work with `SingleCellExperiment` objects.
 
 # Available data sets
 
-The available data sets can be split into two categories.
-The first category contains expression matrices that have been generated by the `r Biocpkg("scRNAseq")` authors 
-from the raw sequencing data for each experiment.
-This includes:
-
-- `ReprocessedFluidigmData()` provides 65 cells from @pollen2014lowcoverage.
-- `ReprocessedTh2Data()` provides 96 T helper cells from @mahata2014singlecell.
-- `ReprocessedAllenData()` provides 379 cells from the mouse visual cortex,
-   which is a subset of the data from @tasic2016adult.
-
-The second category contains expression matrices that were provided by the authors of each study.
-No further reprocessing has been performed other than some cross-checks betweeh the count matrix and the sample metadata.
-
-| Study                 | System           | Number of cells   | Function            |
-|-----------------------|------------------|-------------------|---------------------|
-|@aztekin2019identification | Xenopus tail | 13199             | `AztekinTailData()` |
-|@bach2017differentiation | Mouse mammary gland | 25806        | `BachMammaryData()` |
-|@baron2016singlecell   | Human pancreas   | 8569              | `BaronPancreasData('human')` |
-|@baron2016singlecell   | Mouse pancreas   | 1886              | `BaronPancreasData('mouse')` |
-|@buettner2015computational | Mouse embryonic stem cells | 288 | `BuettnerESCData()` |
-|@campbell2017molecular | Mouse brain      | 21086             | `CampbellBrainData()` | 
-|@chen2017singlecell    | Mouse brain      | 14437             | `ChenBrainData()` |
-|@grun2016denovo        | Mouse haematopoietic stem cells | 1915 | `GrunHSCData()` | 
-|@grun2016denovo        | Human pancreas   | 1728              | `GrunPancreasData()` |
-|@kolodziejczyk2015singlecell | Mouse mebryonic stem cells | 704 | `KolodziejczykESCData()` |
-|@lamanno2016molecular  | Human embryonic stem cells | 1715    | `LaMannoBrainData('human-es')` |
-|@lamanno2016molecular  | Human embryonic midbrain   | 1977    | `LaMannoBrainData('human-embryo')` |
-|@lamanno2016molecular  | Human induced pluripotent stem cells | 337 | `LaMannoBrainData('human-ips')` |
-|@lamanno2016molecular  | Mouse adult dopaminergic neurons | 243 | `LaMannoBrainData('mouse-adult')` |
-|@lamanno2016molecular  | Human embyronic midbrain | 1907 | `LaMannoBrainData('mouse-embryo')` |
-|@lawlor2017singlecell  | Human pancreas   | 638               | `LawlorPancreasData()` |
-|@leng2015oscope        | Human embryonic stem cells | 460     | `LengESCData()` |
-|@lun2017assessing      | 416B cells       | 192               | `LunSpikeInData('416b')` |
-|@lun2017assessing      | Mouse trophoblasts | 192             | `LunSpikeInData('tropho')` |
-|@macosko2015highly     | Mouse retina     | 49300             | `MacoskoRetinaData()` |
-|@marques2016oligodendrocyte | Mouse brain | 5069              | `MarquesBrainData()` | 
-|@messmer2019transcriptional | Human embryonic stem cells | 1344 | `MessmerESCData()` |
-|@muraro2016singlecell  | Human pancreas   | 3072              | `MuraroPancreasData()` |
-|@nestorowa2016singlecell | Mouse haematopoietic stem cells | 1920 | `NestorowaHSCData()` | 
-|@paul2015transcriptional | Mouse haematopoietic stem cells | 10368 | `PaulHSCData()` | 
-|@richard2018tcell      | Mouse CD8+ T cells | 572             | `RichardTCellData()` |
-|@romanov2017molecular  | Mouse brain      | 2881              | `RomanovBrainData()` |
-|@segerstolpe2016single | Human pancreas   | 3514              | `SegerstolpePancreasData()` |
-|@shekhar2016comprehensive | Mouse retina  | 44994             | `ShekharRetinaData()` |
-|@usoskin2015unbiased   | Mouse brain      | 864               | `UsoskinBrainData()` |
-|@tasic2016adult        | Mouse brain      | 1809              | `TasicBrainData()` |
-|@xin2016rna            | Human pancreas   | 1600              | `XinPancreasData()` |
-|@zeisel2015brain       | Mouse brain      | 3005              | `ZeiselBrainData()` |
+The `listDatasets()` function returns all available datasets in `r Biocpkg("scRNAseq")`,
+along with some summary statistics and the necessary R command to load them.
+
+```{r}
+out <- listDatasets()
+```
+
+```{r, echo=FALSE}
+out <- as.data.frame(out)
+out$Taxonomy <- c(`10090`="Mouse", `9606`="Human", `8355`="Xenopus")[as.character(out$Taxonomy)]
+out$Call <- sprintf("`%s`", out$Call)
+knitr::kable(out)
+```
+
+If the original dataset was not provided with Ensembl annotation, we can map the identifiers with `ensembl=TRUE`.
+Any genes without a corresponding Ensembl identifier is discarded from the dataset.
+
+```{r}
+sce <- ZeiselBrainData(ensembl=TRUE)
+head(rownames(sce))
+```
+
+Functions also have a `location=TRUE` argument that loads in the gene coordinates.
+
+```{r}
+sce <- ZeiselBrainData(ensembl=TRUE, location=TRUE)
+head(rowRanges(sce))
+```
 
 # Adding new data sets
 
@@ -109,9 +89,4 @@ and creates a `SingleCellExperiment` object.
 Potential contributors are recommended to examine some of the existing scripts in the package to pick up the coding conventions.
 Remember, we're more likely to accept a contribution if it's indistinguishable from something we might have written ourselves!
 
-As a general rule, 10X Genomics data sets are not suitable for inclusion in this package.
-They are either easy to load (e.g., with functions from the `r Biocpkg("DropletUtils")` package),
-or they are more appropriately obtained with dedicated 10X packages like `r Biocpkg("TENxPBMCData")` or `r Biocpkg("TENxBrainData")`.
-That said, inclusion will be considered if the format has been sufficiently customized by the original authors.
-
 # References