compare {onemap} | R Documentation |
For a given sequence with n markers, computes the multipoint likelihood of all n!/2 orders.
compare(w,n.best=50,tol=10E-6,verbose=FALSE)
w |
an object of class sequence . |
n.best |
the number of best orders to store in object (defaults to 50). |
tol |
tolerance for the C routine, i.e., the value used to evaluate convergence. |
verbose |
if FALSE (default), simplified output is displayed. if
TRUE , detailed output is displayed. |
Since the number n!/2 is large even for moderate values of n, this function is to be used only for sequences with relatively few markers. If markers of types D1, D2 and C (specially in repulsion phase) are mixed in the sequence, this function can be used with up to 5 or 6 markers; otherwise, up to 10 markers will not take a very long time. The multipoint likelihood is calculated according to Wu et al. (2002b) (Eqs. 7a to 11), assuming that the recombination fraction is the same in both parents. Hidden Markov chain codes adapted from Broman et al. (2008) were used.
An object of class compare
, which is a list containing the
following components:
best.ord |
a matrix containing the best orders. |
best.ord.rf |
a matrix with recombination frequencies for the
corresponding best orders. |
best.ord.phase |
a matrix with linkage phases for the best
orders. |
best.ord.like |
a vector with log-likelihood values for the best
orders. |
best.ord.LOD |
a vector with LOD Score values for the best
orders. |
data.name |
name of the object of class outcross with the
raw data. |
twopt |
name of the object of class rf.2pts with the 2-point
analyses. |
Marcelo Mollinari, mmollina@esalq.usp.br
Broman, K. W., Wu, H., Churchill, G., Sen, S., Yandell, B. (2008) qtl: Tools for analyzing QTL experiments R package version 1.09-43
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.
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.
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
marker.type
for details about segregation types and
make.seq
.
## Not run: data(example_out) twopt <- rf.2pts(example_out) markers <- make.seq(twopt,c(12,14,15,26,28)) markers.comp <- compare(markers) markers.comp <- compare(markers,verbose=TRUE) markers.comp ## End(Not run)