onemap (version 1.0-0)

add_drop: Add or Drop Markers From a Sequence

Description

Creates a new sequence adding or dropping markers from a predetermined one.

Usage

add.marker(w, mrks)
drop.marker(w, mrks)

Arguments

w

an object of class sequence.

mrks

a vector containing the markers to be added or removed from the sequence.

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 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.

Examples

data(example_out)
twopt <- rf.2pts(example_out)
all.mark <- make.seq(twopt,"all")
groups <- group(all.mark)
(LG1 <- make.seq(groups,1))
(LG.aug<-add.marker(LG1, c(4,7)))
(LG.red<-drop.marker(LG1, c(1,2,3,5,6)))