setDimMCSlot: SetDimSlot

View source: R/mca.R

setDimMCSlotR 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


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