cpoints: cpoints

In CONFESS: Cell OrderiNg by FluorEScence Signal

Description

It performs the change-point analysis of the variance stabilized adjusted fluorescence signals.

Usage

cpoints(data, thresh, cmethod, sig.level, Q, path.type, seed)

Arguments

data	List. A list of adjusted fluorescence signals in both channels. Typically, the output of transformFluo().
thresh	Integer. The minimum number of values for a cluster re-estimated by the change-point analysis.
cmethod	Character string. The change point method to be used. It can be one of "ECP", (non-parametric) "manualECP" (non-parametric with user-defined numner of change-points) or "PELT" (Pruned Exact Linear Time; parametric).
sig.level	Float. The significance level below which we do not reject a change point.
Q	Integer. The number of change-points to be kept if CPmethod = "manualECP".
path.type	Character vector. A user-defined vector that characterizes the cell progression dynamics. The first element can be either "circular" or "A2Z" or "other". If "circular" the path progression is assummed to exhibit a circle-like behavior. If "A2Z" the path is assumed to have a well-defined start and a well-defined end point (e.g. a linear progression). If "other" the progression is assumed to be arbitrary without an obvious directionality.
seed	Integer. An optional seed number for the Random Number Generator.

Value

A list with the adjusted fluorescence signals and their change-points

CONFESS documentation built on Nov. 8, 2020, 6:05 p.m.