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QGene 4.0:an extensible Java QTL-analysis platform  

2011-05-14 17:07:55|  分类: 数量遗传学 |  标签: |举报 |字号 订阅

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Summary: Of many statistical methods developed to date for quantitative trait locus (QTL) analysis, only a limited subset are available in public software allowing their exploration, comparison and practical application by researchers. We have developed QGene 4.0, a plug-in platform that allows execution and comparison of a variety of modern QTL-mapping methods and supports third-party addition of new ones. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable.

Authors: Roby Joehanes

James C. Nelson
Published in:
· Journal
Bioinformatics archive
Volume 24 Issue 23, December 2008
Oxford University Press Oxford, UK
table of contents doi>10.1093/bioinformatics/btn523

This is the window that appears when you start QGene. It's really just a frame that holds the other windows and provides a menu. Here are the menu items and what they do:

QGene 4.0:an extensible Java QTL-analysis platform - 喜欢吃桃子 - wangyufeng的博客

File

New map

Allows you to specify parameters for simulating a map.

New population

If you've selected an existing map (or data set containing a map) in the Data Manager, allows you to specify parameters for simulating genotype data for that map.

New trait

If you've selected an existing population (or data set containing a population ) in the Data Manager, allows you to specify parameters for simulating one or more traits for that population.

Load data

This is the option you'll use to load into QGene data files in QGene format or any other accepted format from disk. You can also load data files directly from your computer's file manager (such as Windows Explorer) by dragging and dropping their icons onto a QGene window.

Save, Save as

These options will save to disk any dataset in the Data Manager. This may be a simulated map or population, or a data set loaded from a file in another format, or a data set created or modified by the addition of traits. Files may be saved in  qdf, QTL Cartographer, or original (Mac) QGene format. If another output format is desired, please notify the authors, or write an export plugin yourself if you're a Java developer.

Quit

QGene 4.0:an extensible Java QTL-analysis platform - 喜欢吃桃子 - wangyufeng的博客

Analysis

QTL mapping

Opens a window allowing you to apply QTL analysis to a selected data set. You may open as many such windows as memory allows, even on the same data set.

Trait analysis

When a data set containing traits is selected, allows you to view trait distributions and perform other operations; see the manual page.
QGene 4.0:an extensible Java QTL-analysis platform - 喜欢吃桃子 - wangyufeng的博客

Options

Change scan interval

Shows the current QTL interval-map scanning interval and allows you to specify a new one, to be applied to all subsequently opened QTL mapping windows.

Save images as grayscale

If you're preparing images for publication and don't require color, this is the option to use. More about exporting QTL map images...

Toggle look and feel

Try this option to have your windows and controls drawn in native Java style or according to the conventions of your computer's operating system -- the default that is used when QGene is first started.

QGene 4.0:an extensible Java QTL-analysis platform - 喜欢吃桃子 - wangyufeng的博客

Windows and Help menus

These hardly need descriptions -- if you're not sure what an option does, just try it. The Show log window option is useful for reporting bugs or any other problems you may have with QGene.

QGene 4.0:an extensible Java QTL-analysis platform - 喜欢吃桃子 - wangyufeng的博客

Availability: Software and documentation are available at http://coding.plantpath.ksu.edu/qgene. Source code is available on request.

Contact: jcn@ksu.edu

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