diffuseMat: Generic diffusion function

In wjawaid/bglab: Berthold Gottgens lab scRNA seq

Description

Generic diffusion function

Usage

diffuseMat(data, ndims = 4, nn = 0.2, sigma = 12, removeFirst = TRUE,
  bluntDensityCorrection = FALSE, useARPACK = TRUE, normBy = c("Column",
  "Row", "Original"), distfun = NULL)

Arguments

data	Matrix of data with genes in rows and cells in columns.
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
bluntDensityCorrection	Blunt density correction
useARPACK	By default uses rARPACK but can be set to false to use the eigen function from the base package.
normBy	Normalise by Column, row or both.
distfun	A different distance function

Details

Generic diffusion function

Value

List conatining diffusion map.

Author(s)

Wajid Jawaid

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