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(
input.seq,
n.init = 5,
subset.search = c("twopt", "sample"),
subset.n.try = 30,
subset.THRES = 3,
twopt.alg = c("rec", "rcd", "ser", "ug"),
THRES = 3,
touchdown = FALSE,
tol = 0.1,
rm_unlinked = FALSE,
verbose = FALSE
)
An object of class order
, which is a list containing the
following components:
an object of class sequence
containing the "safe" order.
a vector
with
unpositioned markers (if they exist).
a matrix
with LOD-Scores for unmapped markers, if any, for each position in the
"safe" order.
the same as the input value, just for printing.
an object of class sequence
containing the
"forced" order, i.e., the best order with all markers.
name of the object of class onemap
with the raw
data.
name of the object of class rf_2pts
with the
2-point analyses.
an object of class sequence
.
the number of markers to be used in the compare
step
(defaults to 5).
a character string indicating which method should be
used to search for a subset of informative markers for the
compare
step. It is used for backcross, \(F_2\) or RIL
populations, but not for outcrosses. See the Details
section.
integer. The number of times to repeat the subset
search procedure. It is only used if subset.search=="sample"
. See
the Details
section.
numerical. The threshold for the subset search
procedure. It is only used if subset.search=="sample"
. See the
Details
section.
a character string indicating which two-point algorithm
should be used if subset.search=="twopt"
. See the Details
section.
threshold to be used when positioning markers in the
try_seq
step.
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.
tolerance number for the C routine, i.e., the value used to evaluate convergence of the EM algorithm.
When some pair of markers do not follow the linkage criteria,
if TRUE
one of the markers is removed and returns a vector with remaining
marker numbers (useful for mds_onemap and map_avoid_unlinked functions).
A logical, if TRUE its output progress status information.
Gabriel R A Margarido, gramarga@usp.br and Marcelo Mollinari, mmollina@gmail.com
For outcrossing populations, the initial subset and the order in which
remaining markers will be used in the try_seq
step is given by the
degree of informativeness of markers (i.e markers of type A, B, C and D, in
this order).
For backcrosses, F2s or RILs, two methods can be used for
choosing the initial subset: i) "sample"
randomly chooses a number
of markers, indicated by n.init
, and calculates the multipoint
log-likelihood of the \(\frac{n.init!}{2}\) possible orders.
If the LOD Score of the second best order is greater than
subset.THRES
, than it takes the best order to proceed with the
try_seq
step. If not, the procedure is repeated. The maximum number
of times to repeat this procedure is given by the subset.n.try
argument. ii) "twopt"
uses a two-point based algorithm, given by the
option "twopt.alg"
, to construct a two-point based map. The options
are "rec"
for RECORD algorithm, "rcd"
for Rapid Chain
Delineation, "ser"
for Seriation and "ug"
for Unidirectional
Growth. Then, equally spaced markers are taken from this map. The
"compare"
step will then be applied on this subset of markers.
In both cases, the order in which the other markers will be used in the
try_seq
step is given by marker types (i.e. co-dominant before
dominant) and by the missing information on each marker.
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.
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. and Green, P. (1987). Construction of multilocus genetic linkage maps in humans. Proc. Natl. Acad. Sci. USA 84: 2363-2367.
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 genetics 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
make_seq
, compare
and
try_seq
.
# \donttest{
#outcross example
data(onemap_example_out)
twopt <- rf_2pts(onemap_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
# }
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