map {onemap} | R Documentation |
Estimates the multipoint log-likelihood, linkage phases and recombination frequencies for a sequence of markers in a given order.
map(w,tol=10E-6)
w |
an object of class sequence . |
tol |
tolerance for the C routine, i.e., the value used to evaluate convergence. |
Markers are mapped in the order defined in the object w
. If this
object also contains a user-defined combination of linkage phases,
recombination frequencies and log-likelihood are estimated for that
particular case. Otherwise, the best linkage phase combination is also
estimated. 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 sequence
, which is a list containing the
following components:
seq.num |
a vector containing the (ordered) indices of
markers in the sequence, according to the input file. |
seq.phases |
a vector with the linkage phases between markers
in the sequence, in corresponding positions. -1 means there are
no defined linkage phases. |
seq.rf |
a vector with the recombination frequencies between
markers in the sequence. -1 means there are no estimated
recombination frequencies. |
seq.like |
log-likelihood of the corresponding linkage map. |
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. |
Gabriel R A Margarido, gramarga@esalq.usp.br and 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
data(example_out) twopt <- rf.2pts(example_out) markers <- make.seq(twopt,c(30,12,3,14,2)) # correct phases map(markers) markers <- make.seq(twopt,c(30,12,3,14,2),phase=c(4,1,4,3)) # incorrect phases map(markers)