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CLC number: Q348

On-line Access: 2010-07-04

Received: 2009-11-30

Revision Accepted: 2010-03-09

Crosschecked: 2010-05-17

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Journal of Zhejiang University SCIENCE B 2010 Vol.11 No.7 P.512-515


QTLNetworkR: an interactive R package for QTL visualization

Author(s):  Wen-jun Zheng, Jian Yang, Jun Zhu

Affiliation(s):  Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, China, Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia

Corresponding email(s):   jzhu@zju.edu.cn

Key Words:  Visualization, Quantitative trait loci (QTL), QTL mapping, R package, QTLNetworkR

Wen-jun Zheng, Jian Yang, Jun Zhu. QTLNetworkR: an interactive R package for QTL visualization[J]. Journal of Zhejiang University Science B, 2010, 11(7): 512-515.

@article{title="QTLNetworkR: an interactive R package for QTL visualization",
author="Wen-jun Zheng, Jian Yang, Jun Zhu",
journal="Journal of Zhejiang University Science B",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T QTLNetworkR: an interactive R package for QTL visualization
%A Wen-jun Zheng
%A Jian Yang
%A Jun Zhu
%J Journal of Zhejiang University SCIENCE B
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%D 2010
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B0900384

T1 - QTLNetworkR: an interactive R package for QTL visualization
A1 - Wen-jun Zheng
A1 - Jian Yang
A1 - Jun Zhu
J0 - Journal of Zhejiang University Science B
VL - 11
IS - 7
SP - 512
EP - 515
%@ 1673-1581
Y1 - 2010
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B0900384

QTLNetworkR is an r package that aims to provide a user-friendly and platform-independent tool to visualize quantitative trait loci (QTL) mapping results. The graphical functions of the QTLNetworkR are based upon lattice and grid packages, and the graphical user interface (GUI) of the QTLNetworkR is built upon RGtk2 and gWidgetsRGtk2 packages. Six functions are designed to help visualize marker interval, putative QTL, QTL-by-environment interactions, marker interval interactions, epistasis, and the predicted genetic architecture of complex traits. It is especially helpful in profiling results for multiple traits at multiple environments. The current version of QTLNetworkR is able to accept QTL mapping results from QTLNetwork, and it is ready for possible extensions to import results from some other QTL mapping software packages. In addition, we presented a QTL mapping result in rice (Oryza sativa) as an example to describe the features of QTLNetworkR.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


[1]Broman, K.W., Wu, H., Sen, S., Churchill, G.A., 2003. R/qtl: QTL mapping in experimental crosses. Bioinformatics, 19(7):889-890.

[2]Clark, R.M., Wagler, T.N., Quijada, P., Doebley, J., 2006. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nature Genetics, 38(5):594-597.

[3]Doebley, J., 2004. The genetics of maize evolution. Annual Review of Genetics, 38(1):37-59.

[4]Haley, C.S., Knott, S.A., 1992. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity, 69(4):315-324.

[5]Ihaka, R., Gentleman, R., 1996. R: a language for data analysis and graphics. Journal of Computational and Graphical Statistics, 5(3):299-314.

[6]Joehanes, R., Nelson, J.C., 2008. QGene 4.0, an extensible Java QTL-analysis platform. Bioinformatics, 24(23):2788-2789.

[7]Jourjon, M.F., Jasson, S., Marcel, J., Ngom, B., Mangin, B., 2005. MCQTL: multi-allelic QTL mapping in multi-cross design. Bioinformatics, 21(1):128-130.

[8]Kao, C.H., Zeng, Z.B., Teasdale, R.D., 1999. Multiple interval mapping for quantitative trait loci. Genetics, 152(3):1203-1216.

[9]Lander, E.S., Botstein, D., 1989. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics, 121(1):185-199.

[10]Lander, E.S., Green, P., Abrahamson, J., Barlow, A., Daly, M.J., Lincoln, S.E., Newberg, L.A., 1987. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics, 1(2):174-181.

[11]Mackay, T.F., 2001. The genetic architecture of quantitative traits. Annual Review of Genetics, 35(1):303-339.

[12]Manly, K.F., Cudmore, R.H.Jr., Meer, J.M., 2001. Map Manager QTX, cross-platform software for genetic mapping. Mammalian Genome, 12(12):930-932.

[13]Seaton, G., Haley, C.S., Knott, S.A., Kearsey, M., Visscher, P.M., 2002. QTL Express: mapping quantitative trait loci in simple and complex pedigrees. Bioinformatics, 18(2):339-340.

[14]Wang, D.L., Zhu, J., Li, Z.K., Paterson, A.H., 1999. Mapping QTLs with epistatic effects and QTL×environment interactions by mixed linear model approaches. Theoretical and Applied Genetics, 99(7-8):1255-1264.

[15]Wang, S.C., Basten, C.J., Zeng, Z.B., 2006. Windows QTL Cartographer 2.5. Available from http://statgen.ncsu.edu/ qtlcart/WQTLCart.htm

[16]Wright, S., 1980. Genic and organismic selection. Evolution, 34(5):825-843.

[17]Yang, J., Zhu, J., Williams, R.W., 2007. Mapping the genetic architecture of complex traits in experimental populations. Bioinformatics, 23(12):1527-1536.

[18]Yang, J., Hu, C., Hu, H., Yu, R., Xia, Z., Ye, X., Zhu, J., 2008. QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics, 24(5):721-723.

[19]Zeng, Z.B., 1994. Precision mapping of quantitative trait loci. Genetics, 136(4):1457-1468.

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