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From what I understand we first integrate the rna and adt assays seperately using the integrate layers function
IntegrateLayers(
obj,
method= CCAIntegration,
orig.reduction = "pca",
assay = 'RNA',
new.reduction = "integrated.cca.rna"
)
IntegrateLayers(
obj,
method= CCAIntegration,
orig.reduction = "pca",
assay = 'ADT',
new.reduction = "integrated.cca.adt"
)
After this do we combine them using these integrated reductions?
From what I understand we first integrate the rna and adt assays seperately using the integrate layers function
IntegrateLayers(
obj,
method= CCAIntegration,
orig.reduction = "pca",
assay = 'RNA',
new.reduction = "integrated.cca.rna"
)
IntegrateLayers(
obj,
method= CCAIntegration,
orig.reduction = "pca",
assay = 'ADT',
new.reduction = "integrated.cca.adt"
)
After this do we combine them using these integrated reductions?
obj <- FindMultiModalNeighbors(
obj, reduction.list = list("integrated.cca.rna", "integrated.cca.adt"),
dims.list = list(1:30, 1:30), modality.weight.name = "RNA.weight"
)
or do we do a pca, and if so on what.
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