onemap (version 3.0.0)

map: Construct the linkage map for a sequence of markers

Description

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

Usage

map(
  input.seq,
  tol = 1e-04,
  verbose = FALSE,
  rm_unlinked = FALSE,
  phase_cores = 1,
  parallelization.type = "PSOCK",
  global_error = NULL,
  genotypes_errors = NULL,
  genotypes_probs = NULL
)

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 onemap 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.

verbose

If TRUE, print tracing information.

rm_unlinked

When some pair of markers do not follow the linkage criteria, if TRUE one of the markers is removed and returns a vector with remaining marker numbers (useful for mds_onemap and map_avoid_unlinked functions).

phase_cores

number of computer cores to be used in analysis

parallelization.type

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

global_error

single value to be considered as error probability in HMM emission function

genotypes_errors

matrix individuals x markers with error values for each marker

genotypes_probs

table containing the probability distribution for each combination of marker × individual. Each line on this table represents the combination of one marker with one individual, and the respective probabilities. The table should contain four three columns (prob(AA), prob(AB) and prob(BB)) and individuals*markers rows.

Author

Adapted from Karl Broman (package 'qtl') by Gabriel R A Margarido, and Marcelo Mollinari, , with minor changes by Cristiane Taniguti and Bastian Schiffthaler

Details

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.

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)) # correct phases
  map(markers)

  markers <- make_seq(twopt,c(30,12,3,14,2),phase=c(4,1,4,3)) # incorrect phases
  map(markers)
  # }