marker_type: Informs the segregation patterns of markers

In onemap: Construction of Genetic Maps in Experimental Crosses

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, F2s 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.

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

Value

data.frame with segregation types of all markers in the sequence are displayed on the screen.

Author(s)

Gabriel R A Margarido, [e-mail]

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

 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

onemap documentation built on Nov. 26, 2022, 9:05 a.m.