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@@ -213,7 +213,7 @@ library(Seurat)
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counts <- Read10X("path/to/file")
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# Convert count matrix to SingleCellExperiment to run on decontX
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-sce <- SingleCellExperiment(list(counts = counts)).
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+sce <- SingleCellExperiment(list(counts = counts))
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sce <- decontX(sce)
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# Retrieve decontaminated matrix, round to integer, and convert to Seurat object
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@@ -222,6 +222,14 @@ decontaminated.counts <- round(decontaminated.matrix)
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seuratObject <- CreateSeuratObject(decontaminated.counts)
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```
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+Conversely, if you have a Seurat object containing raw count matrix and would like to run decontX, simply retrieve the count matrix, convert to SingleCellExperiment, and run on decontX.
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+
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+```{r seuratIntegration2, eval=FALSE}
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+counts <- seurat@assays$RNA@counts
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+sce <- SingleCellExperiment(list(counts = counts))
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+sce <- decontX(sce)
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+```
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+
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To import datasets into SingleCellExperiment object, the [singleCellTK](https://bioconductor.org/packages/release/bioc/html/singleCellTK.html) package has several importing functions for different preprocessing tools including CellRanger, STARsolo, BUStools, Optimus, DropEST, SEQC, and Alevin/Salmon. For example, the following code can be used as a template to read in the filtered and raw matrices for multiple samples processed with CellRanger:
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