onemap-package {onemap} | R Documentation |
Implements the methodology proposed by Wu et al. (2002a), which uses the maximum likelihood approach to estimate linkage and linkage phases for a mixed set of different marker types containing various segregation patterns. Furthermore, implements the Hidden Markov Model- based approach for constructing multipoint maximum likelihood linkage maps (Wu et al. 2002b). The software was developed to construct genetic maps using full-sib families derived from two outbred parent plants, such as done for example by Garcia et al. (2006), Oliveira et al. (2007) and Oliveira et al. (2008).
Package: | onemap |
Type: | Package |
Version: | 1.0-0 |
Date: | 2009-03-09 |
License: | GNU GENERAL PUBLIC LICENSE (Version 2 or higher) |
Usage of onemap is completely described in a tutorial
distributed with the package. You can look for it in directory
/doc
of the package distribution.
The most important functions are:
read.outcross
for data importing.
rf.2pts
to perform two-point
analyses between all pairs of markers.
marker.type
to check the segregation type of
a marker.
make.seq
to define a sequence of markers,
which are the input of most mapping functions.
group
to assign markers to linkage
groups.
compare
to compare all possible orders
of markers in a sequence.
try.seq
to try a given marker in every
position of a framework of mapped markers.
order.seq
to automate the process of mapping
a sequence of markers, combining compare and try.seq functions.
ripple
to check a set of mapped markers,
looking for (plausible) alternative orders.
map
to construct a map for a sequence
in a given order.
See the complete tutorial distributed along with this package for complete examples (located in directory /doc of the package distribution).
Gabriel R A Margarido, gramarga@esalq.usp.br, Marcelo Mollinari, mmollina@esalq.usp.br and Antonio A F Garcia, aafgarci@esalq.usp.br
Basten, C. J., Weir, B. S. and Zeng, Z.-B. (2005) QTL Cartographer Version 1.17: A Reference Manual and Tutorial for QTL Mapping.
Broman, K. W., Wu, H., Churchill, G., Sen, S., Yandell, B. (2008) qtl: Tools for analyzing QTL experiments R package version 1.09-43
Doerge, R. W. (1996) Constructing genetic maps by rapid chain delineation. Journal of Quantitative Trait Loci 2: 121-132.
Garcia, A. A. F., Kido, E. A., Meza, A. N., Souza, H. M. B., Pinto, L. R., Pastina, M. M., Leite, C. S., Silva, J. A. G., Ulian, E. C., Figueira, A. V. O. and Souza, A. P. (2006) Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases. Theoretical and Applied Genetics 112: 298-314.
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Jiang, C. and Zeng, Z.-B. (1997). Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica 101: 47-58.
Kosambi, D. D. (1944) The estimation of map distance from recombination values. Annuaire of Eugenetics 12: 172-175.
Lander, E. S. and Green, P. (1987). Construction of multilocus genetic linkage maps in humans. Proc. Natl. Acad. Sci. USA 84: 2363-2367.
Lander, E. S., Green, P., Abrahamson, J., Barlow, A., Daly, M. J., Lincoln, S. E. and Newburg, L. (1987) MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174-181.
Lincoln, S. E., Daly, M. J. and Lander, E. S. (1993) Constructing genetic linkage maps with MAPMAKER/EXP Version 3.0: a tutorial and reference manual. A Whitehead Institute for Biomedical Research Technical Report.
Margarido, G. R. A., Souza, A.P. and Garcia, A. A. F. (2007) OneMap: software for genetic mapping in outcrossing species. Hereditas 144: 78-79.
Oliveira, K. M., Pinto, L. R., Marconi, T. G., Margarido, G. R. A., Pastina, M. M., Teixeira, L. H. M., Figueira, A. V. O., Ulian, E. C., Garcia, A. A. F. and Souza, A. P. (2007) Functional genetic linkage map based on EST-markers for a sugarcane (Saccharum spp.) commercial cross. Molecular Breeding 20: 189-208.
Oliveira, E. J., Vieira, M. L. C., Garcia, A. A. F., Munhoz, C. F.,Margarido, G. R.A., Consoli, L., Matta, F. P., Moraes, M. C., Zucchi, M. I., and Fungaro,M. H. P. (2008) An Integrated Molecular Map of Yellow Passion Fruit Based on Simultaneous Maximum-likelihood Estimation of Linkage and Linkage Phases J. Amer. Soc. Hort. Sci. 133: 35-41.
Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002a) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.
Wu, R., Ma, C.-X., Wu, S. S. and Zeng, Z.-B. (2002b). Linkage mapping of sex-specific differences. Genetical Research 79: 85-96