setDimMCSlot {CelliD} | R Documentation |
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.
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