It would be great if I could do something like this with scFeatures.
mySCE is a SingleCellExperiment or SpatialExperiment with an assay called "norm" which contains the normalised data, it also has imageID and cellType in the colData() and spatial coordinates x and y in either the colData or in spatialCoords (if SpatialExperiment).
mySCE <- scFeatures(mySCE,
features = c("proportions", "gene_mean", "L_function"),
assay = "norm",
imageID = "imageID",
cellType = "cellType",
spatialCoords = c("x", "y"))
the function would then output all of the features as assays in a multiassayexperiment so I could get proportions using assay(mySCE, "proportions")
This would make it waaaaaaaaaaay more useable for me.
Bonus points if it could pull at the image/sample specific columns from colData and add them in too.
It would be great if I could do something like this with scFeatures.
mySCE is a SingleCellExperiment or SpatialExperiment with an assay called "norm" which contains the normalised data, it also has imageID and cellType in the colData() and spatial coordinates x and y in either the colData or in spatialCoords (if SpatialExperiment).
mySCE <- scFeatures(mySCE,
features = c("proportions", "gene_mean", "L_function"),
assay = "norm",
imageID = "imageID",
cellType = "cellType",
spatialCoords = c("x", "y"))
the function would then output all of the features as assays in a multiassayexperiment so I could get proportions using assay(mySCE, "proportions")
This would make it waaaaaaaaaaay more useable for me.
Bonus points if it could pull at the image/sample specific columns from colData and add them in too.