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 QTL mapping using the R package R/qtl. It is also possible to create an output to be used with QTLCartographer.

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.

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

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: 
data(fake.f2.onemap)
twopt<-rf.2pts(fake.f2.onemap)
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 "fake.f2.onemap.map" file
write.map(map.list, "fake.f2.onemap.map")

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

require(qtl)
file<-paste(system.file("example",package="onemap"),"fake.f2.onemap.raw", sep="/")
dat1 <- read.cross("mm", file=file, mapfile="fake.f2.onemap.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="fake.f2.onemap")


## End(Not run)

[Package onemap version 2.0-4 Index]