write.map {onemap} | R Documentation |
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.
write.map(map.list, file.out)
map.list |
a map, i.e. an object of class |
file.out |
output map file. |
This function is avaliable only for backcross, F2 and RILs.
Marcelo Mollinari, mmollina@usp.br
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.
## 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)