Description Usage Arguments Details Value Author(s) References See Also Examples
Implements the marker ordering algorithm Unidirectional Growth (Tan & Fu, 2006).
1 | ug(input.seq, LOD = 0, max.rf = 0.5, tol = 1e-04)
|
input.seq |
an object of class |
LOD |
minimum LOD-Score threshold used when constructing the pairwise recombination fraction matrix. |
max.rf |
maximum recombination fraction threshold used as the LOD value above. |
tol |
tolerance for the C routine, i.e., the value used to evaluate convergence. |
Unidirectional Growth (UG) is an algorithm for marker ordering in linkage groups. It is not an exhaustive search method and, therefore, is not computationally intensive. However, it does not guarantee that the best order is always found. The only requirement is a matrix with recombination fractions between markers.
After determining the order with UG, the final map is constructed
using the multipoint approach (function map
).
An object of class sequence
, which is a list containing the
following components:
seq.num |
a |
seq.phases |
a |
seq.rf |
a |
seq.like |
log-likelihood of the corresponding linkage map. |
data.name |
name of the object of class |
twopt |
name of the object of class |
Marcelo Mollinari, mmollina@usp.br
Mollinari, M., Margarido, G. R. A., Vencovsky, R. and Garcia, A. A. F. (2009) Evaluation of algorithms used to order markers on genetics maps. Heredity 103: 494-502.
Tan, Y. and Fu, Y. (2006) A novel method for estimating linkage maps. Genetics 173: 2383-2390.
1 2 3 4 5 6 7 8 9 10 | ## Not run:
#outcross example
data(example.out)
twopt <- rf.2pts(example.out)
all.mark <- make.seq(twopt,"all")
groups <- group(all.mark)
LG1 <- make.seq(groups,1)
LG1.ug <- ug(LG1)
## End(Not run)
|
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