setDimMCSlot: SetDimSlot

In RausellLab/CelliD: Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

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

RausellLab/CelliD documentation built on Jan. 12, 2024, 3:44 a.m.