ziplinR: The main function to project positions from one map to...

In jframi/ziplinR: Project map positions from one map to another based on common markers

The main function to project positions from one map to another

Description

The main function to project positions from one map to another

Usage

ziplinR(map, map1, map2, named.chr = T, map2tomap1 = F, shift.extrem = T,
  exclude = NULL)

Arguments

map	a map containing the positions to be projected. The map format is the same as the one used by Rqtl, ie a list of vectors of positions
map1	the first reference map
map2	the second reference map
map2tomap1	if TRUE the positions of map will be projected from map2 to map1. Default is FALSE
shift.extrem	if TRUE (default) the new map will be shifted in case some positions are projected to negative values
exclude	a vector of marker names to exclude from references, typically showing discrepancies

Value

a map of new projected positions

Author(s)

J.-F. Rami [e-mail]

Examples

data(sorgho_p118)
genomv2<-as.map(genomv2.df)
#create a new dummy map
newmap<-as.map(data.frame(mk=paste("m",1:1000,sep=""),chr=c(rep(1,500),rep(2,500)),Pos=round(c(sort(runif(n=500,min=1,max=1e8)),sort(runif(n=500,min=1,max=1e8))),0)))
newmap.genet<-ziplinR(map=newmap,map1=genomv2,map2=p118.genet,exclude = "SB_06_045",shift.extrem = T)

jframi/ziplinR documentation built on Dec. 6, 2024, 9:37 p.m.