write_map {onemap} | R Documentation |
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 |
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, mmollina@usp.br
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"))
}