how to Seurat::RunUMAP() but run reduction="pca" on subset of features?

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How can I run umap on a seurat object, and specify the features (genes) to use for the initial PCA reduction?

I'm looking for something like what the following [hypothetical] syntax would achieve:

data("pbmc_small")
pbmc_small
# Run UMAP map on first 5 PCs
pbmc_small <- RunUMAP(object = pbmc_small, dims = 1:5, reduction="pca", reduction features= c("CD79A", "MS4A1, TCL1A", "HLA-DQA1", "HLA-DQB1",...))

Where the [non-existent] option "reduction features" specifies the features to use for RunUMAP(...,reduction="pca")


seurat


pca


umap

• 63 views

1 hour ago by


mk

&utrif;

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