try_seq {onemap} | R Documentation |
Try to map a marker into every possible position between markers in a given map
Description
For a given linkage map, tries do add an additional unpositioned marker. This function estimates parameters for all possible maps including the new marker in all possible positions, while keeping the original linkage map unaltered.
Usage
try_seq(input.seq, mrk, tol = 0.1, pos = NULL, verbose = FALSE)
Arguments
input.seq |
an object of class |
mrk |
the index of the marker to be tried, according to the input file. |
tol |
tolerance for the C routine, i.e., the value used to evaluate convergence. |
pos |
defines in which position the new marker |
verbose |
if |
Value
An object of class try
, which is a list containing
the following components:
ord |
a |
LOD |
a |
try.ord |
a |
data.name |
name of the object of
class |
twopt |
name of
the object of class |
Author(s)
Marcelo Mollinari, mmollina@usp.br
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.
Mollinari, M., Margarido, G. R. A., Vencovsky, R. and Garcia, A. A. F. (2009) Evaluation of algorithms used to order markers on genetic maps. Heredity 103: 494-502
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
#outcrossing example
data(onemap_example_out)
twopt <- rf_2pts(onemap_example_out)
markers <- make_seq(twopt,c(2,3,12,14))
markers.comp <- compare(markers)
base.map <- make_seq(markers.comp,1)
extend.map <- try_seq(base.map,30)
extend.map
print(extend.map,5) # best position
print(extend.map,4) # second best position