onemap-package {onemap} | R Documentation |
Implements the methodology proposed by Wu et al. (2002), which uses the maximum likelihood approach to estimate linkage and linkage phases for a mixed set of different marker types containing various segregation patterns. 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) and Oliveira et al. (2007).
Package: | onemap |
Type: | Package |
Version: | 0.1-0 |
Date: | 2007-09-25 |
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.
est.rf.2pts
to perform two-point
analyses between all pairs of markers.
modify.rf.2pts
to update two-point
analyses with different criteria.
arbitr.rf.2pts
to arbitrarily (ad
hoc) define the most probable linkage phase between two markers.
mrktype
to check the segregation type of
a marker.
group
to assign markers to linkage
groups.
extract.group
to ‘extract’ a
linkage group for further analysis.
remove.marker
to drop a marker from a
linkage group.
map
to estimate the genetic map (marker
order and distances) for a given linkage group.
make.map
to arbitrarily define a genetic
map.
est.rf.3pts
to refine a genetic map
using three-point analyses for a triplet of markers.
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
Basten, C. J., Weir, B. S. and Zeng, Z.-B. (2005) QTL Cartographer Version 1.17: A Reference Manual and Tutorial for QTL Mapping.
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.
Haldane, J. B. S. (1919) The combination of linkage values and the calculation of distance between the loci of linked factors. Journal of Genetics 8: 299-309.
Kosambi, D. D. (1944) The estimation of map distance from recombination values. Annuaire of Eugenetics 12: 172-175.
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.
Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.