Distance based Cell LinEAge Reconstruction (DCLEAR)

Il-Youp Kwak (ikwak2@cau.ac.kr) and Wuming Gong (gongx030@umn.edu)

R/DCLEAR is an R package for Distance based Cell LinEAge Reconstruction(DCLEAR). These codes are created during the participation of Cell Lineage Reconstruction DREAM challenge.

DCLEAR Overview

Figure 1. Overview of DCLEAR modeling architecture. Our model is divided into two parts, 1) estimating distance between cells and 2) constructing tree using distance matrix.

Estimating distance between cells

Naive approach would be the hamming distance that simply calculate the edit distance.

However, the previous approach assume every base difference have same weights. For example, two sequences, '00AB0' and '0-CB0', are different at second and third positions. The second position, we have '0' and '-', and the third position, we have 'A' and 'C'.

For '0' and '-', '-' is point missing and it is possibly '0'. Thus it should have lower weight. For 'A' and 'C', During the cell propagation, '0' differentiated to 'A' and '0' differentiated to 'C'. Thus it should have larger weight. We can assign weights as below equation.

And we can approximate unknown weights using training data.

K-mer replacement distance

Constructing tree from the distance matrix

With the previously proposed distance matric, we can construct distance matrix among cells. We can apply tree construction algorithms such as Neighbor-Joining(NJ), FastME.

Usage

• How to use weighted hamming : Link
• How to use kmer_replacement : Colab Link
• Preparation for subchallenge 2 submission : Colab Link
• Preparation for subchallenge 3 submission : link

installation

With 'devtools':

devtools::install_github("ikwak2/DCLEAR")

License

The R/DCLEAR package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3

Presentation

Our talk on the special DREAM session in RECOMB 2020 meeting (https://www.recomb2020.org/) can be found here.