| make.seq {onemap} | R Documentation |
Makes a sequence of markers based on an object of another type.
make.seq(w, arg=NULL, phase=NULL, twopt=NULL)
w |
an object of class rf.2pts, group, compare,
try or order. |
arg |
its value is dependent on the type of object w. For an
object rf.2pts, arg can be the string "all", resulting in
a sequence with all markers in the raw data (generally done for
grouping markers); otherwise, it must be a vector of integers
specifying which markers comprise the sequence. For an object of class
group, arg must be an integer specifying the group. For
a compare object, arg is an integer indicating the
corresponding order (arranjed according to the likelihood); if
NULL (default), the best order is taken. For an object of class
try, arg must be an integer less than or equal to the
length of the original sequence plus one; the sequence obtained will be
that with the additional marker in the position indicated by arg.
Finally, for an order object, arg is a string: "safe"
means the order that contains only markers mapped with the provided
threshold; "force" means the order with all markers. |
phase |
its value is also dependent on the type of w. For an
rf.2pts object, phase can be a vector with user-
defined linkage phases (its length is equal to the number os markers
minus one); if NULL (default), other functions will try to find
the best linkage phases. For example, if phase assumes the
vector c(1,2,3,4), the sequence of linkage phases will be
couple/couple, couple/repulsion, repulsion/couple and
repulsion/repulsion for a sequence of five markers. If w is of class compare or
try, this argument indicates which combination of linkage phases
should be chosen, for the particular order given by argument arg.
In both cases, NULL (default) makes the best combination to be
taken. If w is of class group or order, this
argument has no effect. |
twopt |
a string indicating the name of the object which
contains the two-point information. This does not have to be defined by
the user: it is here for compatibility issues when calling
make.seq from inside other functions. |
An object of class sequence, which is a list containing the
following components:
seq.num |
a vector containing the (ordered) indices of
markers in the sequence, according to the input file. |
seq.phases |
a vector with the linkage phases between markers
in the sequence, in corresponding positions. -1 means there are
no defined linkage phases. |
seq.rf |
a vector with the recombination frequencies between
markers in the sequence. -1 means there are no estimated
recombination frequencies. |
seq.like |
log-likelihood of the corresponding linkage map. |
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 Margarido, gramarga@esalq.usp.br
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.
compare, try.seq,
order.seq and map.
## Not run: data(example_out) twopt <- rf.2pts(example_out) all.mark <- make.seq(twopt,"all") all.mark <- make.seq(twopt,1:30) # same as above, for this data set groups <- group(all.mark) LG1 <- make.seq(groups,1) LG1.ord <- order.seq(LG1) (LG1.final <- make.seq(LG1.ord)) # safe order (LG1.final.all <- make.seq(LG1.ord,"force")) # forced order markers <- make.seq(twopt,c(2,3,12,14)) markers.comp <- compare(markers) (base.map <- make.seq(markers.comp)) base.map <- make.seq(markers.comp,1,1) # same as above (extend.map <- try.seq(base.map,30)) (base.map <- make.seq(extend.map,5)) # fifth position is the best ## End(Not run)