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Add some more things to the object before calling iSEE #84

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Sep 18, 2023
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Add some more things to the object before calling iSEE #84

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14 changes: 13 additions & 1 deletion episodes/04-exploratory-qc.Rmd
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Expand Up @@ -319,7 +319,19 @@ Useful tools for interactive exploratory data analysis for RNA-seq are [Glimma](
## Challenge: Interactively explore our data using iSEE

```{r isee, eval=FALSE}
app <- iSEE(se)
## Convert DESeqDataSet object to a SingleCellExperiment object, in order to
## be able to store the PCA representation
sce <- as(dds, "SingleCellExperiment")

## Add PCA to the 'reducedDim' slot
stopifnot(rownames(pcaData) == colnames(sce))
reducedDim(sce, "PCA") <- as.matrix(pcaData[, c("PC1", "PC2")])

## Add variance-stabilized data as a new assay
stopifnot(colnames(vsd) == colnames(sce))
assay(sce, "vsd") <- assay(vsd)

app <- iSEE(sce)
shiny::runApp(app)
```

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