Description Usage Arguments Details Value Author(s) References See Also Examples
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 posible positions, while keeping the original linkage map unaltered.
1 |
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 |
The diagnostic graphic is made of three figures: i) the top figure
represents the new genetic map obtained with the insertion of the
new marker mrk
on position pos
. If pos = NULL
(default), the marker is placed on the best position i.e. the one
which results LOD = 0.00, which is indicated by a red triangle;
ii) the left bottom figure represents the base map (contained in
input.seq
) on x-axis and the LOD-Scores of the linkage maps
obtained with the new marker mrk
tested at the beginning,
between and at the end of the base map. Actually, it is a graphic
representation of the LOD
vector (see Value
section). The red triangle indicates the best position where the
new marker mrk
should be placed; iii) the right bottom
figure is the non-interactive rf.graph.table
function for the new genetic map (deprecated in BatchMap).
It plots a matrix of pairwise
recombination fractions (under the diagonal) and LOD Scores (upper
the diagonal) using a color scale.
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 |
Marcelo Mollinari, mmollina@usp.br
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## Not run:
#outcrossing example
data(example.out)
twopt <- rf.2pts(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
## End(Not run)
|
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