onemap (version 3.0.0)

write_map: 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)

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.

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.

Author

Marcelo Mollinari,

Details

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

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

# \donttest{
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"))

}
# }