dropByDropone: Drop markers that significantly expand the genetic map.

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

Description

dropByDropone Leverage the results of qtl::droponemarker to find markers that are likely misplaced or erroneous.

Usage

dropByDropone(cross, droponeRes, endMarkerThresh = 12,
  midMarkerThresh = 4, which.map = NULL, map.function = "kosambi",
  re.est.map = F, sex.sp = F, ...)

Arguments

cross	The QTL cross object, with an estimated genetic map
droponeRes	Results from qtl::droponemarker
endMarkerThresh	The ldiff (length increase of map) that causes a marker to be dropped from the map if the marker is at the end/start of a chromosome.
midMarkerThresh	The ldiff (length increase of map) that causes a marker to be dropped from the map.
which.map	If the cross is a 4-way, which sex-specific map should be used? See the column names of the dropone results. Defaults to Ldiff.female, but can be set to Ldiff.male. Ignored if cross is not a 4way.
map.function	If re.est.map = TRUE, the map functions to employ
re.est.map	Should the genetic map be re-estimated?
sex.sp	If re.est.map = TRUE, should a sex-specific map be estimated?
...	Additional arguemnts passed on to est.map if re.est.map = TRUE.

Details

A simple function to parse output from droponemarker postion.

Value

A cross object without markers that caused map expansion > thresholds.

Examples

library(qtlTools)
data(fake.f2)
cross<-fake.f2
## Not run: 
dropone<-droponemarker(cross, map.function = "kosambi")
plot(dropone, lodcolumn = 2)

cross1<-dropByDropone(cross = cross, droponeRes = dropone, endMarkerThresh = 50, re.est.map=T)
plot.map(cross,cross1)

## End(Not run)

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