marker_type function

Informs the segregation patterns of markers

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.

marker_type(input.seq)

Arguments

• input.seq: an object of class sequence.

Returns

data.frame with 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
D2.18	oo x ao	1:1

Examples

data(onemap_example_out)
 twopts <- rf_2pts(onemap_example_out)
 markers.ex <- make_seq(twopts,c(3,6,8,12,16,25))
 marker_type(input.seq = markers.ex) # segregation type for some markers

 data(onemap_example_f2)
 twopts <- rf_2pts(onemap_example_f2)
 all_mrk<-make_seq(twopts, "all")
 lgs<-group(all_mrk)
 lg1<-make_seq(lgs,1)
 marker_type(lg1) # segregation type for linkage group 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

Author(s)

Gabriel R A Margarido, gramarga@gmail.com