.embedSamples_def {CellTrails}R Documentation

DEF: Spectral embedding of samples

Description

For details see embedSamples

Usage

.embedSamples_def(x, nbins = 10, sigma = 0.75, design = NULL)

Arguments

x

A numerical matrix

nbins

Cubic B-spline discretization is used to compute fuzzy mutual information between pairs of samples; nbins defines the number of intervals used for discretization of expression data. (default: 10)

sigma

The mutual information matrix is transformed to an adjacency matrix using a heat kernel; sigma defines the radius of heat kernel (in quantiles; default: sigma = 0.75 which is the third quantile of the mutual information matrix).

design

A numeric matrix describing the factors that should be blocked

Author(s)

Daniel C. Ellwanger


[Package CellTrails version 1.11.0 Index]