order.seq {onemap} | R Documentation |
For a given sequence of markers, this function first uses the compare
function to create a framework for a subset of informative markers. Then, it tries to map
remaining ones using the try.seq
function.
order.seq(w,n.init=5,THRES=3,touchdown=FALSE,tol=10E-5)
w |
an object of class sequence . |
n.init |
the number of markers to be used in the compare step
(defaults to 5). |
THRES |
threshold to be used when positioning markers in the try.seq
step. |
touchdown |
logical. If FALSE (default), the try.seq step is
run only once, with the value of THRES . If TRUE , try.seq
runs with THRES and then once more, with THRES-1 . The latter
calculations take longer, but usually are able to map more markers. |
tol |
tolerance number for the C routine, i.e., the value used to evaluate convergence. |
After running the compare
and try.seq
steps, which result in a
"safe" order, markers that could not be mapped are "forced" into the map,
resulting in a map with all markers positioned.
An object of class order
, which is a list containing the following
components:
ord |
an object of class sequence containing the "safe" order. |
mrk.unpos |
a vector with (possibly) unpositioned markers. |
LOD.unpos |
a matrix with LOD-Scores for unmapped markers, if any,
for each position in the "safe" order. |
THRES |
the same as the input value, just for printing. |
ord.all |
an object of class sequence containing the "forced"
order, i.e., the best order with all markers. |
data.name |
name of the object of class outcross with the
raw data. |
twopt |
name of the object of class rf.2pts with the 2-point
analyses. |
Gabriel R A Margarido, gramarga@esalq.usp.br and Marcelo Mollinari, mmollina@esalq.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.
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
make.seq
, compare
and
try.seq
.
## Not run: data(example_out) twopt <- rf.2pts(example_out) all.mark <- make.seq(twopt,"all") groups <- group(all.mark) LG2 <- make.seq(groups,2) LG2.ord <- order.seq(LG2,touchdown=TRUE) LG2.ord make.seq(LG2.ord) # get safe sequence make.seq(LG2.ord,"force") # get forced sequence ## End(Not run)