onemap (version 2.0-4)

marker.type: Informs the segregation patterns of markers

Description

Informs the type of segregation of all markers from an object of class sequence. For outcross populations it uses the notation by Wu et al., 2002. For backcrosses, \(F_2\) and RILs, it uses the traditional notation from MAPMAKER i.e. AA, AB, BB, not AA and not BB.

Usage

marker.type(input.seq)

Arguments

input.seq

an object of class sequence.

Value

Nothing is returned. Segregation types of all markers in the sequence are displayed on the screen.

Details

The segregation types are (Wu et al., 2002):

Type	Cross	Segregation
A.1	ab x cd	1:1:1:1
A.2	ab x ac	1:1:1:1
A.3	ab x co	1:1:1:1
A.4	ao x bo	1:1:1:1
B1.5	ab x ao	1:2:1
B2.6	ao x ab	1:2:1
B3.7	ab x ab	1:2:1
C8	ao x ao	3:1
D1.9	ab x cc	1:1
D1.10	ab x aa	1:1
D1.11	ab x oo	1:1
D1.12	bo x aa	1:1
D1.13	ao x oo	1:1
D2.14	cc x ab	1:1
D2.15	aa x ab	1:1
D2.16	oo x ab	1:1
D2.17	aa x bo	1:1

References

Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.

See Also

make.seq

Examples

# NOT RUN {
  data(example.out)
  twopts <- rf.2pts(example.out)
  markers.ex <- make.seq(twopts,c(3,6,8,12,16,25))
  marker.type(markers.ex) # segregation type for some markers

  data(fake.f2.onemap)
  twopts <- rf.2pts(fake.f2.onemap)
  all.mrk<-make.seq(twopts, "all")
  lgs<-group(all.mrk)
  lg1<-make.seq(lgs,1)
  marker.type(lg1) # segregation type for linkage group 1

# }