WinQTLCart
Windows QTL Cartographer 2.0
User Manual
? 2007 N.C. State University, Bioinformatics Research Center
Table of Contents
About Windows QTL Cartographer4
WinQTLCart features
(4)
Compatible programs and formats
(4)
System requirements
(5)
Installing, uninstalling, upgrading
(5)
Using WinQTL - a high-level overview5
When to use WinQTLCart
(6)
WinQTLCart Windows & Menus7
Main window - Menus
(7)
(7)
Main window - Menus - File
Main window - Menus - Edit
(8)
(8)
Main window - Menus - View
Main window - Menus - Method
(8)
Main window - Menus - Tools
(9)
(9)
Main window - Menus - Help
Chromosome graph display - Menus
(9)
Chromosome graph - Menus - File
(9)
Chromosome graph - Menus - View
(10)
Chromosome graph - Menus - Setting
(10)
Main window tour
(11)
Main window - Tree Pane
(12)
Main window - Form Pane
(13)
Main window - Data Pane
(14)
Graph window - Menus
(14)
Graph window - Menus - File
(14)
Graph window - Menus - Chrom
(15)
Graph window - Menus - Traits
(15)
Graph window - Menus - Effects
(15)
Graph window - Menus - Tools
(16)
Graph window - Menus - Setting
(16)
One-page display window - Menus
(17)
One-Page window - Menus - File
(17)
One-Page window - Menus - View
(17)
One-Page window - Menus - Setting
(18)
Graph window - Procedures
(18)
Tracing coordinates on the graph
(20)
Selecting traits for graph display
(21)
Selecting chromosomes for graph display
(21)
Setting display parameters
(22)
(24)
Setting a test hypothesis
Showing QTL information
(25)
WinQTLCart Procedures26 Setting the working directory
(26)
Importing and exporting
(26)
Importing files
(26)
Exporting source data and results
(29)
Exporting source data to QTL Cartographer
(30)
Exporting source data to an MCD file
(30)
Exporting results from the Graph window
(31)
(31)
Working with source data files
Opening source data files
(32)
Working with a source file's marker genotype data
(32)
Working with a source file's traits values
(33)
Working with a source file's basic information
(33)
Working with source file's individual information
(35)
(37)
Working with source file's chromosome information
Working with source file's trait information
(38)
Working with source file's other trait information
(38)
(39)
MCD file format
Creating a new source data file from raw data
(43)
Creating simulation data
(50)
(54)
Single-marker analysis
Setting threshold levels (IM & CIM)
(55)
Setting threshold levels manually
(56)
Setting threshold levels via permutations
(56)
Interval Mapping
(57)
Running interval mapping analysis
(57)
Composite Interval Mapping
(59)
Running composite interval mapping analysis
(59)
Multiple Interval Mapping
(62)
About the MIM form
(62)
Creating MIM initial model
(64)
(65)
Regression options
CIM search option
(66)
MIM search option
(68)
Refining the MIM model
(69)
Multiple-trait MIM
(69)
About the Mt-MIM form
(69)
(71)
Mt-MIM Control File
Mt-MIM Functions
(72)
Bayesian Interval Mapping
(73)
(74)
Running Bayesian interval mapping analysis
Multiple-trait analysis
(75)
Drawing a chromosome tree
(75)
Adding QTL positions to the chromosome graphics
(77)
Tutorials78 Import data files
(78)
Import data - INP format
(78)
Using Emap function
(78)
Import data - OUT format
(78)
Import data - MapMaker format
(78)
Import data - Excel format
(79)
Simulation source data file
(79)
Create new source data file
(79)
Single marker analysis
(80)
Interval mapping
(80)
Composite interval mapping
(80)
Multiple-trait analysis
(81)
Multiple Interval Mapping
(81)
Bayesian interval mapping
(81)
(82)
Result manipulation
Technical notes82 Troubleshooting
(82)
(82)
WinQTLCart cannot import Map information from selected file
Invalid file or wrong format messages
(82)
Technical Support
(83)
(83)
Credits & acknowledgements
Index84
About Windows QTL Cartographer
WinQTLCart features
Windows QTL Cartographer maps quantitative trait loci (QTL) in cross populations from inbred lines.WinQTLCart includes a powerful graphic tool for presenting mapping results and can import and export data in a variety of formats.WinQTLCart incorporates many of the modules found in its command-line sibling, QTL Cartographer ,and provides a graphical interface to many of QTL Cartographer's features.WinQTLCart implements the following statistical methods:
?Single-marker analysis ?Interval mapping ?Composite interval mapping ?Bayesian interval mapping ?Multiple interval mapping ?Multiple trait analysis ?Multiple trait MIM analysis Features
?Supports various QTL mapping methods
?View, copy, and print graphs
?Includes an interface to help you build a source data file that WinQTLCart can use for analysis ?Import data from Mapmaker / QTL and Microsoft Excel formats
?Export graph data to Windows Excel format
?View, copy, and print
chromosome information graphically
?Produce a simulation data file
Compatible programs and formats
WinQTLCart can import and export data files in a variety of formats. Import success depends on the data file's format. Some data may need to be formatted manually before WinQTLCart can import it.
Related topics
Creating a new source data file Troubleshooting import errors 54
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Importing files Exporting source data and results
System requirements
?WinQTLCart can run on the following operating systems: Windows 95, 98, ME, NT, 2000, and XP.?Internet Explorer 3.x or better should be installed to view WinQTLCart's online help.
?Because some WinQTLCart windows are quite large, the suggested minimum monitor resolution is 1024x768.
?10MB free disk space for program files.
?258MB RAM.
?Any mouse or pointing device supported by Windows.
Installing, uninstalling, upgrading
Installing
To install, double-click the WQTLSetup.exe file and follow the prompts. The default install directory is C:\NCSU\WinQTLCart2.5, though you can specify a different directory.
The installer places a shortcut to the Windows QTL Cartographer program on your PC's Desktop,labeled WinQTLCart. Double-click the icon to run the program.
Uninstalling
To uninstall, run the Add/Remove Programs control panel and select Windows QTL Cartographer from the installed programs list.
Upgrading
If you have a prior version of WinQTLCart already on your PC, simply run the installer program.Upgrading to a new version of WinQTLCart does not overwrite your working files. However, the upgrade will replace the sample files that are part of the WinQTLCart distribution.
Note
You should close current running version of WinQTLCart first before installing the upgrading version. Using WinQTL - a high-level overview
Your goals in using WinQTLCart may include preparing data for publication or continued research into possible QTL sites.
Step 1—Preparing your source data Your data files may come from another program or they may exist as raw data files. For WinQTLCart to work with your files, they need to conform to the program's .MCD file format . Review that file, as well as the other files included in the WinQTLCart distribution, such as the .QRT, .QPE, and other files.These are all text files that you can view in any text editor.
Or, you may not have any data files or any data ready for import. You may instead want to use WinQTLCart to create simulation data to try out some hypotheses to view potential results. See these topics for more information: MCD file format
, Creating a new source data file from raw
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Step 2—Bringing data into WinQTLCart
WinQTLCart can import map and cross data files from MapMaker/QTL, QTL Cartographer, and Microsoft Excel. As part of the import, WinQTLCart runs verification checks against the data. If the data does not conform to the accepted format, WinQTLCart displays an error message that should indicate the source of the problem.See these topics for more information: Importing files , WinQTLCart cannot import Map information from selected file , Invalid file or wrong format messages Your source data may not have come from another program, but may instead exist as raw source files.In that case, using WinQTLCart's Create a New Source File command steps you through all of the steps needed to translate the raw data into a readable form. The new source file will conform to WinQTLCart's MCD file format.
See these topics for more information: Creating a new source data file from raw data
, MCD file
format Step 3—Analyzing data using QTL Mapping Methods
With WinQTLCart able to view the data, you can then select any of seven different analysis methods.The end result for some of these methods is another MCD file, but in most cases the process will create a .QRT result file that WinQTLCart can use to graph QTL information.See these topics for more information: Single-marker analysis , Interval Mapping , Composite Interval Mapping , Multiple Interval Mapping , Bayesian Interval Mapping , Multiple-trait Analysis , Multiple-trait MIM.
Step 4—Viewing results and graphs
WinQTLCart can present your data in graphics suitable for publication. You can show all
chromosomes and their intervals in one display, while the Graph window display offers many parameters to help you fine-tune the visualization.
See these topics for more information: Drawing a chromosome tree , Graph Window tour Step 5—Saving and exporting results
You can save your source data in .MCD format and your results files in .QRT format so you can work with them later in WinQTLCart. You can also export your results to other selected formats.
See these topics for more information: Exporting source data and results , Exporting results from the Graph window , Exporting source data to an MCD file , Exporting source data to QTL Cartographer When to use WinQTLCart
You can use WinQTLCart for any kind of data that is cross populations from inbred lines. WinQTLCart is a particularly powerful tool when you want to explore your results graphically.
Prior to doing experiments, you could use WinQTLCart to explore some "what-if" scenarios in planning your experimental design. In WinQTLCart, you can create simulation data and then vary parameters setting to explore various QTL models.
However, if you're working on a repetitive task that would be better off scripted, you may want to turn to QTL Cartographer , WinQTLCart's command-line sibling. For example, if you have expression data with thousands of features, you might want to run interval mapping on each feature, which would take a long time. This task can be automated via a shell script and made to run overnight. The results can 268282
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then be imported into WinQTLCart and its graphs charted.
Also, some analyses (such as multiple interval mapping) may take a long time to complete and can be sent to the background using the command-line version.WinQTLCart Windows & Menus
Main window - Menus Menus in Main window include File , Edit , View , Method , Tools , and Help
. Main window - Menus - File
Icon Command
Function New Create a new source data file from raw text files.
See Creating a new source data file Open Open a data file, result file or text file.
Source data files you can open in WinQTLCart have the .MCD
extension. Results files have the .QRT extension. Files with
any other extension are opened as text files.
Close Close the currently selected file. (The currently selected .MCD
file's name is in the title bar and highlighted in the Tree pane).
Save As Save the currently active source data to a file with mcd format
or a file with Microsoft Excel format.
Import
Import files in a variety of formats. See the importing files
topic Simulation Opens the Simulate Data dialog. See creating a simulation
data file Export Export the selected file to a different format. See Exporting
source data and results Print
Print the selected file in data pane.Print Setup
Opens Windows' Print Setup dialog box.Recently used files
WinQTLCart displays the last 6 data files you've worked with.Exit Closes WinQTLCart.
If you have unsaved data, you'll be prompted to save it.
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Main window - Menus - Edit Command Function Copy
Copy selected text in
Data pane to the Windows clipboard.
Select All Click in the Data pane and then choose this command to select all text in
the data pane. Enables you to easily select and copy the text to a separate file.
Main window - Menus - View Icon Command Function
Source Data Summary
Summarizes statistical information of active source data file and displays in Text window. Visualize Result View result file in the Graph window. See Graph
Window tour Toolbar Select to toggle the Toolbar display.
Status bar
Select to toggle the Status bar display.
Main window - Menus - Method
Icon Command
Function Single Marker
Analysis
Displays the Single Marker Analysis form.Interval Mapping Displays the Interval Mapping form.
Composite Interval
Mapping
Displays the Composite Interval Mapping form . Multiple Interval
Mapping
Displays the Multiple Interval Mapping form. Click "OK" button to start MIM analysis and click "MtMIM"button to choose multiple-trait MIM analysis. Multiple Trait
Analysis
Displays the Multiple Trait Analysis form.Bayesian Interval
Mapping Displays the Bayesian Interval Mapping form.
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Main window - Menus - Tools
Icon Command
Function Set Working directory Set the default working directory. See Setting the working
directory Draw chromosome graph
Show and print graphic displays of chromosomes from the
Current active .MCD file. See Drawing a chromosome tree
Copy between trait and otrait Copy normal trait to Other trait (category trait) or vise verse. Delete markers of same position
Delete markers that have the same position in a chromosome and only keep one marker. Notepad Opens Notepad. Use Notepad as a convenient text editor to help format source data files.
Calculator
Open the Windows Calculator accessory. Main window - Menus - Help
Icon Command
Function Help Topics Opens Windows help file of WinQTLCart. About WinQTLCart Display About dialog of WinQTLCart. You can open WinQTLCart upgrade site in this dialog.
Click on any item at Main window to open the
context-sensitive help content.
Chromosome graph display - Menus
Open a mcd source data file. From the Main window, select Tools>DrawChrom to draw the trees of chromosome graph and markers in a single large window that is suitable for copying to an image program for later editing or printing for publication.
Menus in Chromosome graph display window include File , View , and Setting .
Chromosome graph - Menus - File
Command
Function Copy to Clipboard…Copies content in window to the clipboard.
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Print Graphic…Print the graph.
Exit Close the window and return to the Main window.
Chromosome graph - Menus - View
Command Function
Proportion of Marker Number Show length of chromosome graph in proportion of marker number
Proportion of Chromosome Len Show length of chromosome graph in proportion of chromosome length in cM
Next Page >>Show next page of the graph if there are multiple pages.
First Page Show First page of the graph.
Add QTL Positions Display QTL positions in the graph.
Chromosome graph - Menus - Setting
Command Function
Select Chromosomes Select chromosomes to be showed in graph.
Show Chromosome Name Toggle display between chromosome names or chromosome
labels produced by WinQTLCart.
Font Size >>Increase font size of graph.
Font Size < Space Between >>Increase space between chromosomes. Space Between < Chromosome Name >>Increase font size of chromosome names. Chromosome Name < Column Number >>Increase the number of chromosome displayed horizontally. Column Number < horizontally. Main window tour When you start up Windows QTL cartographer, the program's Main window displays. From top to bottom, here's what you see: 1.Title bar. Shows the name of the selected source data file. 2.Menu bar . 3.Toolbar with one-click access to the program's major functions. Hover the pointer over a button to see a brief description of that command. The button's function is also described in the Status bar at the bottom of the window. 4.Tree pane for file management. Lists open files and organizes files under various category names (Source Files, Text Files, Results Files). 5.Form pane for displaying and controlling analysis of source data files. The form pane contents change based on the analysis method you select. 6.Data pane for displaying data of currently selected file. 7.The Status bar displays a variety of system messages; select View>Status bar to toggle its display. Click on each node in the tree pane or hover the pointer over a toolbar button or menu command to see the displayed message. The right area of the status bar also displays the current date and time, and also displays CAP, NUM, or SCRL if the Caps Lock, Num Lock, or Scroll Lock keys have been pressed. ?Double-click on a category name in the Tree pane to open files of that type. ?Left-click on a .MCD filename to make that the active source data file on which to run an analysis. ?Right-click on a filename to see appropriate commands for that file. 7121314 Main window - Tree Pane The Main Window's Tree pane allows you to manage open files. The following table describes the many different options available via left-click, right-click, and double-click operations. Source file selected with right-click options displayed Tree Item Action Function Message window Left-click Displays WinQTLCart startup message in the data pane. Tree Item Action Function Source files root Double-click Open a source data file (.MCD) Right-click>Open a File Open a source data file (.MCD) Tree Item Action Function Result files root Double-click Open a result file (.QRT) Right-click>Open File Open a result file Tree Item Action Function Text files root Double-click Open a text file (.TXT). Right-click>Open File Open a text file Tree Item Action Function .MCD file Left-click Show file contents in the Data pane and set as current working .MCD file Double-click Open the .MCD file in Notepad Right-click options… >Open File Open a new source data file >Open with Notepad Open the .MCD file in Notepad >Refresh Re-load the file after modification >Single Marker Start single marker analysis >Interval Mapping Start interval mapping >Composite IM Start composite interval mapping >Multiple Traits Start multiple traits analysis >Multiple IM Start multiple interval mapping >Bayesian IM Start Bayesian interval mapping Tree Item Action Function .QRT file Left-click Show this result file in text format via the Data pane . Double-click Open the QRT file in the Graph window Right-click options… >Open File Open a new result file >Open with Notepad Open the .QRT file with Notepad >Refresh Re-load the file after modification >Close File Close the result file >Graphic Dialog Open the .QRT file in the Graph window Tree Item Action Function .TXT file Left-click Show this text file in the Data pane Double-click Open the text file with Notepad Right-click options… >Open File Open a new text file >Open with Notepad Open the .TXT file with Notepad >Refresh Re-load the file after modification >Close File Close the text file.Main window - Form Pane The Form pane is the control panel you use to analyze your source data. It serves as a dashboard that presents a lot of information about your source data file at a glance. (The Form pane is keyed to the .MCD source data file only; it does not show information for any other file format.) This "control panel" changes based on the analysis method you select. For each analysis method,WinQTLCart displays different parameters and controls that help you control the analysis. When you first open WinQTLCart, you see the standard Source Data File Information form. Most of the options are disabled because no source data file has been loaded. Select an analysis method from the drop down list in the Analysis box on the right to begin working with the data. When you have opened a file, WinQTLCart enables the buttons and controls on the Source Data File Information form. These enable you to perform some basic manipulations to the source data (such as 141814 add traits, map information, etc.) Forms and disabled commands When you select an analysis method, WinQTLCart assumes you want to keep working with that method until you save your data or cancel the analysis. If you select the Interval Mapping (IM) method,WinQTLCart disables several toolbar and menu commands (such as the other analysis methods, setting the working directory, and so on). You need to either save your data or press the Cancel button on the IM form to leave the IM analysis mode. Leaving an analysis method re-displays the Source Data File Information pane. See the Source data file information topic and the topics for each analysis method for the appropriate screen shot relevant to that method. Main window - Data Pane The large pane under the Form pane displays the content of the active data or results file in text format. You cannot edit the displayed information from this pane. However, you can select the text with your cursor and copy the selected text to the clipboard. For .MCD source data files, WinQTLCart color-codes the data so you can easily determine what are comments, labels, headers, and so on. Graph window - Menus From the Main window, select View>Visualize Result to display the result file (*.qrt) in result graph window. Menus in Graph window include File , Chrom , Traits , Effects , Tools , and Setting . In addition to the toolbar and menu commands, some functions are available by right-clicking on the graph. Graph window - Menus - File Command Function Open QTL Result File Open a result file. Files with the .QRT extension are considered result files. Import QTL Result Graphic Adds a new graph to the current display. Files with the .QRT extension are considered result files. Note: The added result file should have same chromosome number and marker number as original one. You could add more than one new graph. Copy Graphic to Clipboard Copies the graph to the Windows clipboard. Save As New Name Save the file under a different name in .QRT format. You may want to do this if you plan to work with the results in a later WinQTLCart session. 3113141515151616 Save As Text File Save the results as a text file. You may want to do this if you plan to use the text file in another program. Save As Excel File Save the data as an Excel file. Use Excel's charting capabilities to draw the graph. Print Graphic Print the graphic to a selected printer. Exit Closes the Graph window. If you have unsaved data, you'll be prompted to save it. Graph window - Menus - Chrom Command Function Next Chrom >> Display the next chromosome in the file. Prev Chrom << Display the previous chromosome in the file. Select Chroms…Choose the chromosomes you want to graph. You can also change the order of the chromosome display. See Selecting chromosomes for graph display. Show All Chroms Shows all chromosomes in the file in a single graph. Graph window - Menus - Traits Command Function Next Trait >> Display the next trait in the file. Prev Trait < Select Trait(s)…Choose the traits you want to graph. See Selecting traits for graph display. Show All Traits Shows all traits in the file in a single graph. Graph window - Menus - Effects Command Function Show Additive Effect Display additive effect graph at bottom of window. This is on by default for new Graph windows. 21 Show Dominant Effect Display dominant effect graph at bottom of window if cross type is SF n or RF n. Show Values of R2Display R2 value graph at bottom of window. Show Values of TR2Display TR2 value graph at bottom of window. Show Values of S Display S value graph at bottom of window. One Standard Deviation Normalize the additive and dominant effect in one standard deviation. Graph window - Menus - Tools Command Function Display One Page Format Show the graph information in a smaller, one-page format, for publication purposes. See One-page display window - Menus for more information. Show QTLs information Display QTL information from a simulation parameter file or summary QTL peaks. See Showing QTL information. Graph window - Menus - Setting Command Function Set Display Parameters…Allows you to customize the graph display. See Setting display parameters. Set Test Hypothesis…Display result of different tests, such as H1:H3. See Setting a test hypothesis. Show Graph in LR/LOD Scale Toggles between LR and LOD scale displays. Look for LR or LOD at the top of the y-axis line. Black and White/Color Graph Toggle between color and black-and-white display. Use black-and-white graphs for publication. Color/White Background Activate a color or white background; might be useful for printing or to provide better contrast for color graph lines. Hide/Show Threshold Lines Toggle display. Show Horizontal Grids Toggle display. Show Vertical Grids Toggle display. 17 25 22 24 Show Trait Names and Legends Toggle display. If traits are present, WinQTLCart defaults to showing legends on the right side of the graph. Use Set Display Parameters to switch the legends to above the graph. Turn the trait name display on when you're loading more than one result file into a graph. Show Marker Names Toggle display. Show Chromosome Names Toggle display. Trace Coordinate in Graphic Provides coordinates for a specific point on the graph. See Tracing coordinates on the graph. One-page display window - Menus From the Graph window, select Tools>Display One Page Format to display the graphs in a single, large, scrolling window that is suitable for copying to an image program for later editing or printing for publication. The chromosomes and traits shown in the one-page display depends on the Select Chroms and Select Traits settings in the Graph window. Menus in One-page display window include File, View, and Setting. One-Page window - Menus - File Command Function Copy to Clipboard…Copies content in window to the clipboard. Print Graphic…Print the graph. Quit Close the window and return to the Graph window. One-Page window - Menus - View Command Function Show Frame Puts a border around the graph(s). LR Proportion Graph heights according to LR values. Show Color Graphic Toggle display of colors (axis lines remain black). Show Threshold Line Toggle display of threshold line. 22 20 21 21 171718 Show Marker Number Toggle display of marker numbers. Row Number>>Increase graph number in a row by 1. Row Number< Column Number>>Increase graph number in a column by 1. Column Number< One-Page window - Menus - Setting Command Function HSpace Between >>Increase horizontal space between chromosomes. HSpace Between < VSpace Between >>Increase vertical space between chromosomes. VSpace Between < Title Font Size >>Increase title size. Title Font Size < Graph window - Procedures To see the Graph window, open a WinQTLCart results file (with a .QRT extension) by click the Result button on the Main window's toolbar. The Graph window opens, presenting a graphical overview of the results file data. From this window you can: ?Spot the location of QTLs. A graph peak that extends past the threshold line is the site of a QTL. ?Load multiple results files at one time and compare them. This could be useful when comparing the results of the same dataset pushed through different analysis methods and parameters. From top to bottom, here's what you see: 1.Title bar. Shows the name of the selected results data file. You can have multiple results files loaded and multiple Graph windows open at a time. 2.Menu bar 3.Toolbar with one-click access to the program's major functions. Hover the pointer over a button to see a brief description of that command. 4.The large graph charts the data as a LOD (or LR) score profile. The higher the LOD, the greater the evidence for a QTL. 5.The smaller graph at the bottom is the QTL effects window, showing additive or dominant effects or R2 or TR2 or S values. Graph window tips ?You can add several result files so they display at the same time on the current graph. You might want to run your data through the IM, CIM, and MIM analysis methods, for example, and then pull them all into the same graph to see how they compare. ?Peaks above the threshold line indicate a QTL. ?A high LOD value on the graph indicates a good QTL candidate. ?Right-click on the graph to see appropriate commands. (Commands described in the Graph window-Menus topic.) ?You can minimize the Graph window to the bottom of the Main window; a small bit of the title bar is visible. ?You can have the same result file open in several windows at the same time. This might be useful if you're testing various viewing parameters. To do this, minimize the current Graph window, go back to the Main window, ensure the result file is still active, and click the Graph toolbar button. Related topics 14 14