repRipple: Method to improve a genetic map.

In jtlovell/qtlTools: Data Processing and Plotting in Association with R/qtl

Description

repRipple iteratively runs ripple, returning a cross object with the best order.

Usage

repRipple(cross, chr = NULL, window = 5, method = "countxo",
  verbose = T, map.function = "kosambi", sex.sp = F,
  clean1st = FALSE, ripVerb = TRUE, ...)

Arguments

cross	The qtl cross object to search
chr	The chromosome to scan. Can be a vector of chromosome names or a single name.
window	The window size passed on to ripple
method	The method passed on to ripple
verbose	logical, should updates be reported?
map.function	If re.est.map = TRUE, what map function should be used?
...	Additional arguments passed to qtl::ripple
re.est.map	Should the map be re-estimated after drop.similar.markers?
error.prob	If re.est.map = TRUE, what error probability should be used?

Value

A new cross object with the optimal rippled marker order

Examples

## Not run: 
set.seed(42)
map<-sim.map(len = c(50,20), n.mar = c(20,40), include.x=FALSE)
cross0<-sim.cross(map, n.ind=50, type="f2", map.function="kosambi")
## Mess up the order on chr1
mars<-1:nmar(cross0)[1]
set.seed(42)
badorder<-order(jitter(mars, factor = 10))
cross0<-switch.order(cross0, chr = 1, order = badorder,
                     error.prob=0.001, map.function="kosambi")
newmap<-est.map(cross0, error.prob=0.001, map.function="kosambi")
cross0 <- replace.map(cross0, newmap)
cross0<-est.rf(cross0)
cross1<-repRipple(cross0, chr = 1, error.prob=0.001, map.function="kosambi",window = 6)
plot.rf(cross0, chr = 1, main = "recombination fractions before ripple")
plot.rf(cross1, chr = 1, main = "recombination fractions after ripple")

## End(Not run)

jtlovell/qtlTools documentation built on May 20, 2019, 3:14 a.m.