marker.type: Informs the segregation patterns of markers
In BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species

Description Usage Arguments Details Value Author(s) References See Also Examples

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, F2s and RILs, it uses the traditional notation from MAPMAKER i.e. AA, AB, BB, not AA and not BB.

1	marker.type(input.seq)

input.seq

an object of class sequence.

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
D2.18	oo x ao	1:1

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

Gabriel R A Margarido, gramarga@gmail.com

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.

make.seq

  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