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readme.md

ToolSeg 1.2 Software User Manual

1. Introduction

ToolSeg is an open-source, cross-platform Java application that integrates simulation data generation and segmentation achievement. The methods in the system include HMM, PCF, FastPCF, CBS, CLT and Lasso. It not only can be used for comparison between the methods, as well as meeting the needs of the actual segmentation. Most importantly, we will be staging structured. Each segment corresponding method parameters can be adjusted to facilitate users find problems. The input to be segmented can be the data generated by users or the input data that has the certain format. To meet with diverse needs and applications in the cancer research community, ToolSeg not only output .txt file of segmentation result that can be used for further analysis, such as estimates purity and ploidy, but also outputs graphical results that help intuitive understanding of the effect of segmentation. The software and source code of ToolSeg could be downloaded from https://gitee.com/w3STeam/ToolSeg. An example of use is provided.

2. Software System Requirement

The Java Runtime Environment (JRE) version 1.8 or higher is required to be installed and configured properly. JRE could be downloaded at http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html

3. Installation

Step 1: Download a Java IDE and an up-to-date Java Development Kit (JDK). Java SE 1.8 could be downloaded at http://www.oracle.com/technetwork/java/javase/downloads/index.html, as is shown in Figure 1.

Step 2: Install both software using the installation wizards. It is recommended to install the JDK first. Figure 1.Java SE download

Step 3: Download two Zip packages ToolSeg.zip and test_data.zip from https://gitee.com/w3STeam/ToolSeg/attach_files. Then unzip these files to a local folder.

Step 4: Now, enter the folder and click the "start.bat " to run the program in Windows, as is shown in Figure 2. (or run command “java -jar ToolSeg.jar” in Linux.)

Figure 2.Run the project

Step 5: Fast run.

  1. select an input path
  2. load data
  3. select an aogorithm
  4. segment

4. Usage

Figure 3.The GUI

The GUI contains two modules:Input Selection, Algorithms, as is shown in Figure 3.

1) Input Selection Module

The first module is “Input Selection”, where user can choose the input data they need.

There are two data sources users can choose.

The first data source is “Data Generate”, by which, users can generate datas they like. They can generate datas by random, by multi-template or by template shift. They can set the datas’ format. As shown in the figure 8,we set a data that has four segments. Their lengths are respectively 300, 300, 300, 300. Their segment values are respectively 1, 2, 3, 4. Their segment variances are respectively 0.4, 0.4, 0.4, 0.4. And their contaminations are all 0.5. Click “Generate”, the data will be generated,as shown in figure 4.

Click “Show”, we can see the figure, as shown in Figure 6. Click “Clear”, the data generated will be cleared. Click “Save”, the data genereted will be saved as .txt file in the path “..//data”.

Figure 4. Input Selection Module

Figure 5.Data generated

Figure 6. Data’s figure

Another source is the data input by users. Users can choose the input path and the output path, as shown in figure 7. They also can choose whether the input data is used to be tested. The input file should be .txt file like this way:

chrId Loci CNValue

1 0 1.123846

1 1 1.057979

1 2 1.061475.....

chrId is the serial number of Chromosome. Loci is the position of copy number. CNValue is the copy number value.

g

Figure 7.Input data

2) Algorithms Module

Another module is “Algorithms”, where user can choose the algorithm they like, as is shown in Figure 8.

Figure 8.Algorithms Module

The top is “Preprocess”, the left of which is “outliers handling”. You can set the range of the “outliers handling” and choose whether you want to do “outliers handling”. The right is “Transformation”. You can choose only one of the three transformations. “Bypass” means that you don’t want to transform the data and process directly. “Log2” and “Pow2” respectively mean that the data will be transformed by taking a logarithm of 2 and 2 times square.

The bottom is algorithms. There are seven algorithms that can be chosen, “CBS”, “PCF”, “FastPCF”, “BACOM”, “HMM”, “Lasso” and “DBS”, all of which have their corresponding parameters that can be set. Click an algorithm, and you can set corresponding parameters.

For CBS and BACOM: As shown in Figure 9 and 10, “minLength” means the minimum length of segment. It can influence the speed and accuracy of the algorithm. While minLength is smaller, the result is more accurate. While it can slow down the speed of algorithm. “minStep” means The step length when traversing the copy number sequence. For CBS, it involves permutation test, so user can adjust “permutation times”. For BACOM, it involves Center Limit Theory, “pvalue“ is the threshold to judge whether isolates the theory.

Figure 9.CBS Figure 10.BACOM

For PCF and FastPCF: As shown in Figure 11 and 12, “gama” stands for the fixed penalty. PCF utilizes penalized least squares regression to determine a piecewise constant fit to the data, introducing a fixed penalty γ > 0 for any difference in the fitted values of two neighboring observations induces an optimal solution of particular relevance to copy number data.

Figure 11. PCF Figure 12. FastPCF

For HMM: As shown in Figure 13, “Center Probability” stands for the probability that in transition probability matrix, a state to maintain existing state probability. Probability are divided into ten parts. You just have to set center probability takes how much.

Figure 13.HMM

For Lasso: As shown in Figure 14, “lamda” is a constant for L1 regression. “tolerance” means when the difference of result of twice calculation is less than tolerance, calculation finish. “maxIter” is the number of iterations of the algorithm.

Figure 14.Lasso

For DBS: As shown in Figure 15, “minLength” means the minimum length of segment. “pvalue“ is the threshold to judge whether isolates the theory. “lamda” is a constant for L1 regression.

Figure 15.DBS

When the data, the algorithm and their parameters all are prepared, you can choose “Segment” or “TestAll”, as is shown in Figure 16. “Segment” means segmenting by current algorithm, and “TestAll” means segmenting by all algorithms.

Figure 16.Segment and TestAll

After segmented, the result will be saved as a .png picture for every algorithm in the path ..//Pictures. For example, the result of HMM is shown in Figure 17. When “TestAll”, the results of all algorithms will also be saved as a .png picture in the path ..//Result, as is shown in Figure 18. All results will be shown in the console, as is shown in Figure 19.

Figure 17.Picture of HMM

Figure 18. Picture of all results

Figure 19.Picture of console

3)Batch processing

When selecting the data input by users, users can choose whether to batch process, as shown in figure 24. When users choose to batch process, the input file should be .txt file and the content should be like this way:

.\data\testdata2\LTestdata_20161026_151708.txt

.\data\testdata2\LTestdata_20161026_152635.txt

.\data\testdata2\R_Testdata_20161026_151627.txt

.\data\testdata2\R_Testdata_20161026_153220.txt

Here, each .txt file must be one of the above input files. Figure 20.Picture of batch processing

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We propose such toolbox and implement it an open source Java package called ToolSEG to generate realistic DNA copy number profiles with known truth. Five typical method has been assessed on synthetic data and real copy number profiles: HMM, CBS, PCF, Lasso, DBS. spread retract
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