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)