try.seq {onemap} | R Documentation |
For a given linkage map and an additional unpositioned marker, this function estimates parameters for all possible maps including the new marker, while keeping the original linkage map unaltered.
try.seq(input.seq, mrk, tol=10E-2, draw.try=FALSE, pos=NULL, verbose=FALSE) ## S3 method for class 'try' print(x,j=NULL, ...)
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. |
draw.try |
if |
pos |
defines in which position the new marker |
verbose |
if |
x |
an object of class |
j |
if |
... |
further arguments, passed to other methods. Currently ignored. |
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. 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
## 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 #F2 example data(fake.f2.onemap) twopt <- rf.2pts(fake.f2.onemap) all.mark <- make.seq(twopt,"all") groups <- group(all.mark) LG3 <- make.seq(groups,3) LG3.ord <- order.seq(LG3, subset.search = "twopt", twopt.alg = "rcd", touchdown=TRUE) LG3.ord safe.map<-make.seq(LG3.ord,"safe") extend.map <- try.seq(safe.map,64) extend.map (new.map<-make.seq(extend.map,14)) # best position #Display diagnostic graphics try.seq(safe.map,64,draw.try=TRUE) #best position (default) try.seq(safe.map,64,draw.try=TRUE,pos=13) #second best position try.seq(safe.map,64,draw.try=TRUE,pos=4) #wrong position #Trying to position an unliked marker try.seq(safe.map,66,draw.try=TRUE) #note the inconsistencies in the graphic ## End(Not run)