map {onemap} | R Documentation |
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
)
Arguments
input.seq |
an object of class |
tol |
tolerance for the C routine, i.e., the value used to evaluate convergence. |
verbose |
If |
rm_unlinked |
When some pair of markers do not follow the linkage criteria,
if |
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. |
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.
Value
An object of class sequence
, which is a list containing the
following components:
seq.num |
a |
seq.phases |
a |
seq.rf |
a |
seq.like |
log-likelihood of the corresponding linkage map. |
data.name |
name of the object of class |
twopt |
name of the object of class |
Author(s)
Adapted from Karl Broman (package 'qtl') by Gabriel R A Margarido, gramarga@usp.br and Marcelo Mollinari, mmollina@gmail.com, with minor changes by Cristiane Taniguti and Bastian Schiffthaler
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
Examples
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)