write_map: Write a genetic map to a file

In onemap: Construction of Genetic Maps in Experimental Crosses

Write a genetic map to a file

Description

Write a genetic map to a file, base on a given map, or a list of maps. The output file can be used as an input to perform QTL mapping using the package R/qtl. It is also possible to create an output to be used with QTLCartographer program.

Usage

write_map(map.list, file.out)

Arguments

map.list	a map, i.e. an object of class sequence with a predefined order, linkage phases, recombination fraction and likelihood or a list of maps.
file.out	output map file.

Details

This function is available only for backcross, F2 and RILs.

Value

file with genetic map information

Wang S., Basten, C. J. and Zeng Z.-B. (2010) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC.

Author(s)

Marcelo Mollinari, [e-mail]

References

Broman, K. W., Wu, H., Churchill, G., Sen, S., Yandell, B. (2008) qtl: Tools for analyzing QTL experiments R package version 1.09-43

Examples

data(mapmaker_example_f2)
twopt<-rf_2pts(mapmaker_example_f2)
lg<-group(make_seq(twopt, "all"))

##"pre-allocate" an empty list of length lg$n.groups (3, in this case)
maps.list<-vector("list", lg$n.groups)

for(i in 1:lg$n.groups){
  ##create linkage group i
  LG.cur <- make_seq(lg,i)
  ##ordering
  map.cur<-order_seq(LG.cur, subset.search = "sample")
  ##assign the map of the i-th group to the maps.list
  maps.list[[i]]<-make_seq(map.cur, "force")

  ##write maps.list to ".map" file
  write_map(maps.list, tempfile(fileext = ".map"))

}

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