map: Construct the linkage map for a sequence of markers
In BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species

Description Usage Arguments Details Value Author(s) References See Also Examples

Estimates the multipoint log-likelihood, linkage phases and recombination frequencies for a sequence of markers in a given order.

1	map(input.seq, tol = 1e-04, verbosity = FALSE, phase.cores = 1)

`input.seq`	an object of class `sequence`.
`tol`	tolerance for the C routine, i.e., the value used to evaluate convergence.
`verbosity`	Controls verbosity of phase. Currently can only be set to "phase"
`phase.cores`	Number of parallel cores used to estimate linkage phases. Should not be higher than 4.

Markers are mapped in the order defined in the object input.seq. 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 that there are no defined linkage phases.
`seq.rf`	a `vector` with the recombination frequencies between markers in the sequence. `-1` means that 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.

Adapted from Karl Broman (package 'qtl') by Gabriel R A Margarido, gramarga@usp.br and Marcelo Mollinari, mmollina@gmail.com

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

make.seq

  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)