setDimMCSlot {CelliD} | R Documentation

## SetDimSlot

### Description

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.

### Usage

    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", ...)

### Arguments

`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

### Value

Seurat or SingleCellExperiment object with MC stored in the reduction slot

[Package CelliD version 1.2.1 Index]