ug {onemap} | R Documentation |
Implements the marker ordering algorithm Unidirectional Growth (Tan & Fu, 2006).
ug(input.seq, LOD=0, max.rf=0.5, tol=10E-5)
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. Next is an adapted excerpt from Mollinari et al (2009) describing the UG algorithm:
Based on the R (recombination fraction) matrix, the distance between all m loci is calculated by d_ij = r_ij + (2/n_ij) Sum_k r_ik r_jk, for every k, with r_ij > r_ik, r_ij > r_jk, and n_ij individuals. The value T_ij = 2 d_ij - (Sum_{k != i} d_ik + Sum_{k != j} d_jk) is calculated for every i < j. The terminal end of the map is defined by taking the pair of markers (f, g) that presents the smallest value of T. The pair (f, g) is then denoted locus m + 1 and its distance to the remaining markers is determined by d_im+1 = (1/2)(d_if + d_ig - d_fg) if (d_if + d_ig) > d_fg, if not, d_im+1 = 0. The calculation W_im+1 = (m-2) d_im+1 - Sum_{k != i} d_ik is also performed and the locus that minimizes the value W_im+1 (called locus h) is placed on the map. The partial resultant map is f-g-h if d_fh > d_gh or h-f-g otherwise. Considering k = 2, the partial distance of the map with the remaining markers is updated: d_im+k = min(d_im+k-1, d_ij). The value W_im+k = (m-k-1) d_im+k - Sum_{k != i} d_ik is calculated and the locus that minimizes W is added to the map. The last two steps are repeated, taking k = 3, ..., m-1 to obtain the complete map.
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.
## 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) #F2 example data(fake.f2.onemap) twopt <- rf.2pts(fake.f2.onemap) all.mark <- make.seq(twopt,"all") groups <- group(all.mark) LG1 <- make.seq(groups,1) LG1.ug <- ug(LG1) LG1.ug ## End(Not run)