onemap (version 2.1.1)

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(input.seq, LOD = NULL, max.rf = NULL, verbose = TRUE)

Arguments

input.seq

an object of class sequence.

LOD

a (positive) real number used as minimum LOD score (threshold) to declare linkage.

max.rf

a real number (usually smaller than 0.5) used as maximum recombination fraction to declare linkage.

verbose

logical. If TRUE, current progress is shown; if FALSE, no output is produced.

Value

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

data.name

name of the object of class onemap that contains the raw data.

twopt

name of the object of class rf.2ts used as input, i.e., containing 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.

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 input.seq. If not using NULL, the new values override the ones in object input.seq.

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

# NOT RUN {
  data(example_out)
  twopts <- rf_2pts(example_out)

  all.data <- make_seq(twopts,"all")
  link_gr <- group(all.data)
  link_gr
  print(link_gr, details=FALSE) #omit the names of the markers

# }