reDoCross: Run a set of functions that improve the genetic map

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

Description

reDoCross Drop close markers, re-order markers via ripple, then re-check for close markers. Returns a cross object with improved marker order and overly dense marker regions removed.

Usage

reDoCross(cross, window = 5, min.distance = 1,
  map.function = "kosambi", sex.sp = F, verbose = T,
  initialEstMap = TRUE, ...)

Arguments

cross	The QTL cross object.
window	Passed to ripple. Smaller values (e.g. 3) run more quickly but explore fewer possible marker orders. Larger values (e.g. 6) should only be used on maps with few markers. Large numbers of markers with large windows will take a long time.
min.distance	The minimum distance between markers in the final map. If two markers are closer than this value, drop the one with fewer NAs and better segregation distortion.
map.function	The map function to pass on to est.map
sex.sp	Should sex-specific maps be estimated in a 4-way cross? Passed on to est.map.
verbose	Should updates be printed ot the terminal?
initialEstMap	Should the map be estimated before any functions are run?

Details

If any chromosomes are sex-specific, re-class such chromosomes after running newLG: using class(cross$geno[["Xchrom"]]) <- "S" or whatever. The new map has arbitrary cM positions where each marker is separated by 10cM. Run est.map to get true cM positions.

Value

A cross object with markers reordered.

Examples

library(qtlTools)
data(fake.f2)
cross<-fake.f2
## Not run: 
map=est.map(cross, map.function = "haldane")
cross=replace.map(cross, map)
cross2<-reDoCross(cross, map.function = "haldane")
plot.map(cross, cross2)

## End(Not run)

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