Methods for bulk, spatial and merged objects #58
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Click the link below to download the manuscript build as a ZIP file. |
| These genes are used to calculate library-aware principal components with `batchelor::multiBatchPCA()`. | ||
| The top 50 principal components were selected and used to calculate UMAP embeddings for the merged object. | ||
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| If any libraries included in the ScPCA project contain additional ADT data, the ADT data is also merged and stored in the `altExp` slot of the merged `SingleCellExperiment` object. |
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Do we also want to say that if any libraries in the project don't have ADT, they will still be there but with NA values? Is that overkill?
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I feel like that might be overkill. I think the point here is that if there was ADT data to begin with it will also be present in the merged object.
Co-authored-by: Stephanie Spielman <[email protected]>
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Click the link below to download the manuscript build as a ZIP file. |
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LGTM!
While you're here though, can you fix (or try to fix...) these two citations that I found in the HTML build?
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The
STARreference is missing a colon in@doi:
ScPCA-manuscript/content/04.methods.md
Line 79 in 231954c
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Honestly not sure why this
miQCreference doesn't render properly, but if you can figure it out feel free to fix! But it'll get fixed eventually either way.
ScPCA-manuscript/content/03.results.md
Line 61 in 231954c
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Click the link below to download the manuscript build as a ZIP file. |
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The overall content here looks good. I had a few minor order changes, and thoughts about when we want to delve into details of implementation vs. just presenting the process. But nothing I need to see again for now, as I am sure these will come up in round-robin.
| - combining counts data and metadata | ||
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| Merged objects are created with the `merge.nf` workflow within `scpca-nf`. | ||
| This workflow takes as input the processed `SingleCellExperiment` objects in a given ScPCA project output by `scpca-nf` and creates a single merged `SingleCellExperiment` object containing gene expression data and metadata from all libraries in that project. |
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I feel like the fact that the SCEs come from scpca-nf is implied, and removing that clause makes the sentence flow a bit more smoothly.
| This workflow takes as input the processed `SingleCellExperiment` objects in a given ScPCA project output by `scpca-nf` and creates a single merged `SingleCellExperiment` object containing gene expression data and metadata from all libraries in that project. | |
| This workflow takes as input the processed `SingleCellExperiment` objects in a given ScPCA project and creates a single merged `SingleCellExperiment` object containing gene expression data and metadata from all libraries in that project. |
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I don't know that it's necessarily implied so I think for methods purposes it's better to be specific, even if it makes the sentence a little clunkier.
Co-authored-by: Joshua Shapiro <[email protected]>
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Click the link below to download the manuscript build as a ZIP file. |
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Click the link below to download the manuscript build as a ZIP file. |
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Click the link below to download the manuscript build as a ZIP file. |
Closes #41
Closes #43
This PR adds the methods for processing bulk and spatial data and then also creating the merged object. I was unsure about the level of detail for the merged workflow, since there's not much too the actual merging other than we combine things. We could mention that we use
cbind, etc, but I didn't think that was totally necessary. I'm curious what others think.Also, please check to make sure I'm not missing any important references that we should include.
Tagging @jashapiro for review of bulk and spatial and @sjspielman for review of merged objects.