onemap (version 0.1-1)

group: Assign markers to linkage groups

Description

Identifies linkage groups of markers, using results from two-point (pairwise) analysis and the transitive property of linkage.

Usage

group(w)
## S3 method for class 'group':
print(x, detailed=TRUE, \dots)

Arguments

w

an object of class rf.2pts.

x

an object of class group.

detailed

logical. If FALSE, only a small summary of the linkage groups is printed. If TRUE (default), the names of markers in each linkage group are also displayed.

...

further arguments, passed to other methods. Currently ignored.

Value

• Returns an object of class group, which is a list containing the following components:
• marnames
  marker names, according to the input file.
• n.mar
  total number of markers.
• LOD
  minimum LOD Score to declare linkage.
• max.rf
  maximum recombination fraction to declare linkage.
• n.groups
  number of groups found.
• groups
  number of the linkage group to which each marker is assigned.
• name
  name of the object of class rf.2pts used as input, i.e., containing the information used to assign markers to linkage groups.

Details

Thresholds used to group markers, i.e., minimum LOD Score and maximum recombination fraction, are defined in object w.

References

Lincoln, S. E., Daly, M. J. and Lander, E. S. (1993) Constructing genetic linkage maps with MAPMAKER/EXP Version 3.0: a tutorial and reference manual. A Whitehead Institute for Biomedical Research Technical Report.

See Also

est.rf.2pts, modify.rf.2pts and arbitr.rf.2pts

Examples

data(example_out)
  twopts <- est.rf.2pts(example_out)

  link_gr <- group(twopts)
  link_gr