optClust: optimizing clustering for single-cell copy number

Description Usage Arguments Value Examples

View source: R/optClust.R

Description

The optClust is a simple attempt to set a threshold on where to cut the an hclust tree. The aim is to maximize the number of cluster with multiple-cells while minimizing the number of one-cell clusters.

Usage

1
optClust(cnr, opt.range = seq(0.005, 0.6, by = 0.005))

Arguments

cnr

a cnr bundle

opt.range

range of tree heights that need to be optimized

Value

Returns a matrix where rows are the heights in the opt.range, and three columns.

One-cell specifies the number of clusters with only one cell, Multi-cell specifyies the number of clusters with multiple cells (>=2), and

A good threshold is one that minimizes the one-cell cluster, and maximizes the

Examples

1
2
3
4
5
6
7
8
9
data(cnr)

cnr <- phyloCNR(cnr)

optClust(cnr, opt.range = seq(0, 0.3, by = 0.05))

#for micro-optimization

optClust(cnr, opt.range = seq(0, 0.2, by = 0.001))

SingerLab/gac documentation built on Aug. 14, 2021, 10:57 a.m.