group {onemap}R Documentation

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, LOD=NULL, max.rf=NULL)

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

Arguments

w an object of class sequence.
LOD a (positive) real number used as minimum LOD score to declare linkage.
max.rf a real number (usually smaller than 0.5) used as maximum recombination fraction to declare linkage.
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.

Details

If the arguments specifying thresholds used to group markers, i.e., minimum LOD Score and maximum recombination fraction, are NULL (default), the values used are those contained in object w. If not using NULL, the new values overridden the ones in object w.

Value

Returns an object of class group, which is a list containing the following components:

data.name name of the object of class outcross that contains the raw data.
twopt name of the object of class rf.2ts used as input, i.e., containign information used to assign markers to linkage groups.
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 linkage groups found.
groups number of the linkage group to which each marker is assigned.

Author(s)

Gabriel R A Margarido, gramarga@esalq.usp.br

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

rf.2pts and make.seq

Examples

  data(example_out)
  twopts <- rf.2pts(example_out)
  
  all.data <- make.seq(twopts,"all")
  link_gr <- group(all.data)
  link_gr

[Package onemap version 1.0-1 Index]