onemap (version 3.0.0)

seeded_map: Construct the linkage map for a sequence of markers after seeding phases

Description

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

Usage

seeded_map(
  input.seq,
  tol = 1e-04,
  phase_cores = 1,
  seeds,
  verbose = FALSE,
  rm_unlinked = FALSE,
  parallelization.type = "PSOCK"
)

Value

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.

Arguments

input.seq

an object of class sequence.

tol

tolerance for the C routine, i.e., the value used to evaluate convergence.

phase_cores

The number of parallel processes to use when estimating the phase of a marker. (Should be no more than 4)

seeds

A vector given the integer encoding of phases for the first N positions of the map

verbose

A logical, if TRUE it output progress status information.

rm_unlinked

When some pair of markers do not follow the linkage criteria, if TRUE one of the markers is removed and map is performed again.

parallelization.type

one of the supported cluster types. This should be either PSOCK (default) or FORK.

Author

Adapted from Karl Broman (package 'qtl') by Gabriel R A Margarido, and Marcelo Mollinari, . Modified to use seeded phases by Bastian Schiffthaler

Details

Markers are mapped in the order defined in the object input.seq. The best combination of linkage phases is also estimated starting from the first position not in the given seeds.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.

References

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

See Also

make_seq

Examples

# \donttest{
  data(onemap_example_out)
  twopt <- rf_2pts(onemap_example_out)

  markers <- make_seq(twopt,c(30,12,3,14,2))
  seeded_map(markers, seeds = c(4,2))
# }