repPickMarkerSubset: Method to improve an estimated genetic map.
In jtlovell/qtlTools: Data Processing and Plotting in Association with R/qtl

Description Usage Arguments Value Examples

repPickMarkerSubset finds the best marker within a cM window.

1 2	repPickMarkerSubset(cross, chr = NULL, na.weight = 2, sd.weight = 1, min.distance = 1, verbose = TRUE)

`cross`	The qtl cross object to search
`chr`	The chromosome to scan. Can be a vector of chromosome names or a single name. If NULL, run on all chromosomes.
`na.weight`	Same as sd.weight, but for the number of NAs. Only used if cross is not a 4way.
`sd.weight`	The weighting of segregation distortion rank in dropping a marker. Higher values relative to na.weight increase the weight of the sd rank. Setting a value of 0 removes sd as a factor in choosing the best marker. Only used if cross is not a 4way.
`min.distance`	Logical, should markers on the ends of the chromosomes always be retained?
`verbose`	Logical, should updates be printed?

A new cross object with the similar markers dropped.

set.seed(42)
library(qtlTools)
map<-sim.map(len = c(50,20), n.mar = c(20,30), include.x=FALSE)
cross0<-sim.cross(map, n.ind=50, type="f2", map.function="kosambi",
   error.prob=.01, missing.prob = .05)
cross0<-est.rf(cross0)
cross1<-repPickMarkerSubset(cross0)
par(mfrow=c(2,1))
plot.map(cross0, cross1, main = "comparison of full and culled maps")