diffuse-SCD-method: Diffusion Maps

Description Usage Arguments Details Value Author(s)

Description

Diffusion map dimensionality reduction

Usage

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## S4 method for signature 'SCD'
diffuse(object, ndims = 4, nn = 0.2, sigma = NULL,
  removeFirst = TRUE, useARPACK = TRUE, distfun = NULL)

Arguments

object

Single Cell Data object

ndims

Number of dimensions required if using ARPACK otherwise all will be returned

nn

Number of nearest neighbours. Can be set to 1

sigma

Default NULL. Parameter for Gaussian kernel.

removeFirst

Remove the non informative first eigen vector

useARPACK

By default uses rARPACK but can be set to false to use the eigen function from the base package.

distfun

A distance function.

Details

Diffusion map dimensionality reduction as performed by Florian Buettner / Fabian Theis Diffusion map dimensionality reduction

Value

Single Cell Data object with diffusion map

Author(s)

Wajid Jawaid


wjawaid/bglab documentation built on May 4, 2019, 6:33 a.m.