make.seq {onemap} | R Documentation |
Create a sequence of markers
Description
Makes a sequence of markers based on an object of another type.
Usage
make.seq(input.obj, arg=NULL, phase=NULL, twopt=NULL)
Arguments
input.obj |
an object of class rf.2pts , group , compare ,
try or order .
|
arg |
its value depends on the type of object input.obj . 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 (arranged 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 input.obj . For an
rf.2pts object, phase can be a vector with user-
defined linkage phases (its length is equal to the number of 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 input.obj 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 input.obj 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.
|
Value
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 that there are
no defined linkage phases.
|
seq.rf |
a vector with the recombination frequencies between
markers in the sequence. -1 means that 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.
|
Author(s)
Gabriel Margarido, gramarga@gmail.com
References
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.
See Also
compare
, try.seq
,
order.seq
and map
.
Examples
## 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)
[Package
onemap version 2.0-4
Index]