Convert SpatialExperiment Object to Seurat Object
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cathalgking ▴ 10
@0dc78e90
Last seen 11 months ago
Australia

I have a 10x Visium experiment that was aligned with Space Ranger. There is 4 images/samples and each output contains the standard ''/outs/'' folder with image, matrix, tissue positions etc. I read the data into a SpatialExperiment (spe) with the below code.

  1. I would like to convert my SpatialExperiment object to a Seurat object for some downstream analyses. I know that there is functionality to convert a SingleCellExperiment object to a Seurat object with as.SingleCellExperiment(x) but does something similar exist for a Spatial experiment conversion to a Seurat object? When I try to use that function on my spe I get the Error shown below.
  2. Or, is there a way to read in my multiple image/sample experiment into a Seurat object at once as is done with the read10xVisium() function below for a SpatialExperiment?
samples <- c("~/A1count/outs",
             "~/B1count/outs",
             "~/C1count/outs",
             "~/D1count/outs")

sample_ids = c("A1count", "B1count", "C1count", "D1count")

spe <- read10xVisium(
  samples = samples,
  sample_id = sample_ids,
  type = "sparse",
  data = "raw",
  images = "lowres",
  load = TRUE
)

Error in UseMethod(generic = "as.SingleCellExperiment", object = x) : no applicable method for 'as.SingleCellExperiment' applied to an object of class "c('SpatialExperiment', 'SingleCellExperiment', 'RangedSummarizedExperiment', 'SummarizedExperiment', 'RectangularData', 'Vector', 'Annotated', 'vector_OR_Vector')"

scuttle scater seurat SpatialExperiment • 1.1k views
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