RunMCDMAP: Run DiffusionMap on MCA cell and feature coordinates

Description Usage Arguments Value Examples

View source: R/mcaAndReduction.R

Description

Run DiffusionMap on MCA cell and feature coordinates

Usage

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RunMCDMAP(X, reduction, features, dims, reduction.name, ...)

## S3 method for class 'Seurat'
RunMCDMAP(X, reduction = "mca", features = NULL,
  dims = seq(50), reduction.name = "mcdmap", assay = DefaultAssay(X),
  ...)

## S3 method for class 'SingleCellExperiment'
RunMCDMAP(X, reduction = "MCA",
  features = NULL, dims = seq(50), reduction.name = "MCDMAP", ...)

Arguments

X

Seurat or SingleCellExperiment object

reduction

Which dimensionality reduction to use, must be based on MCA.

features

Character vector of feature names to subset feature coordinates. If not specified will take all features available from specified reduction Loadings.

dims

A vector of integers indicating which dimensions to use with reduction embeddings and loadings for distance calculation.

reduction.name

name of the created dimensionlaity reduction, default set to "mca" for Seurat and "MCA" for SCE.

...

other arguments passed to methods or DiffusionMap

assay

Seurat Asssay slot name.

Value

Seurat or SingleCellExperiment object with MCDMAP stored in the reduction slot

Examples

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Cortalak/cellID documentation built on Aug. 3, 2020, 9:01 p.m.