onemap (version 2.1.1)

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)

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 avaliable 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

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

Examples

# NOT RUN {
# }
# NOT RUN {
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 "mapmaker_example_f2.map" file
write_map(map.list, "mapmaker_example_f2.map")

##Using R/qtl
##you must install the package  'qtl'
##install.packages("qtl")

require(qtl)
file<-paste(system.file("example",package="onemap"),"mapmaker_example_f2.raw", sep="/")
dat1 <- read.cross("mm", file=file, mapfile="mapmaker_example_f2.map")
newmap <- est.map(dat1, tol=1e-6, map.function="kosambi")

(logliks <- sapply(newmap, attr, "loglik"))
plot.map(dat1, newmap)

##Using R/qtl to generate QTL Cartographer input files (.map and .cro)
write.cross(dat1, format="qtlcart", filestem="mapmaker_example_f2")

# }
# NOT RUN {
# }