In its earlier version, the software implemented 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, to building genetic maps in outcrossing species. After, it was modified to also using a Hidden Markov Model approach for constructing multipoint maximum likelihood linkage maps (Wu et al. 2002b). It was then applied in several studies, such as Garcia et al. (2006), Oliveira et al. (2007) and Oliveira et al. (2008). Nowadays, the latest versions (2.0-3) was fully modified to also handle with backcrosses, F_2 and recombinant inbred lines (RIL) populations, allowing fully integration with software for QTL mapping, such as R/qtl and QTL Cartographer. OneMap can read and export files to this packages, and also from the widely used software MAPMAKER.
| Package: | onemap |
| Type: | Package |
| Version: | 2.0-3 |
| Date: | 2012-12-06 |
| License: | GNU GENERAL PUBLIC LICENSE (Version 3) |
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.
read.mapmaker for importing data from a
MAPMAKER raw file.
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.seq to check a set of mapped markers,
looking for (plausible) alternative orders.
map to construct a map for a sequence
in a given order.
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