as.SpatialExperiment | R Documentation |
Convert Object to SpatialExperiment
Convert GeoMxSet Object to SpatialExperiment
as.SpatialExperiment(x, ...)
## S3 method for class 'NanoStringGeoMxSet'
as.SpatialExperiment(
x,
normData = NULL,
coordinates = NULL,
forceRaw = FALSE,
...
)
x |
GeoMxSet object to convert |
... |
Arguments passed to other methods |
normData |
assay containing normalized data |
coordinates |
X and Y coordinates of each ROI, format: c(X,Y) |
forceRaw |
should raw data be forced into SpatialExperiment, not recommended |
SpatialExperiment containing GeoMx data
datadir <- system.file("extdata", "DSP_NGS_Example_Data",
package = "GeomxTools")
demoData <- readRDS(file.path(datadir, "/demoData.rds"))
target_demoData <- aggregateCounts(demoData[1:1000,1:10])
target_demoData <- normalize(target_demoData, "quant")
seurat_demoData <- as.SpatialExperiment(target_demoData,
normData = "exprs_norm",
forceRaw = FALSE)
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