Description Usage Arguments Value
Integrate MCA in Seurat and SingleCellExperiment Dimensionlity reduction Slot. It will set also a small parameter inside the dimensionality reduction object to signal if it is a MCA or not.
1 2 3 4 5 6 7 8 9 | setDimMCSlot(X, cellEmb, geneEmb, stdev, reduction.name, ...)
## S3 method for class 'Seurat'
setDimMCSlot(X, cellEmb, geneEmb, stdev = NULL,
reduction.name = "mca", assay = DefaultAssay(X), ...)
## S3 method for class 'SingleCellExperiment'
setDimMCSlot(X, cellEmb, geneEmb,
stdev = NULL, reduction.name = "MCA", ...)
|
X |
Seurat or SingleCellExperiment object |
cellEmb |
cell coordinates returned by MCA |
geneEmb |
feature coordinates returned by MCA |
stdev |
eigen value returned by MCA |
reduction.name |
name of the created dimensionlaity reduction, default set to "mca" for Seurat and "MCA" for SCE. |
... |
other arguments passed to methods |
assay |
Seurat assay slot |
Seurat or SingleCellExperiment object with MC stored in the reduction slot
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