pheno2geno (version 1.4.0)

markerPlacementPlot: Plot number of markers selected.

Description

Plot number of markers selected with different thresholds.

Usage

markerPlacementPlot(population, placeUsing=c("qtl","correlation"), 
    thrRange=c(1,5,1),cross,verbose=FALSE)

Arguments

population

An object of class population. See create.population for details.

placeUsing

How position of the new markers on the saturated map should be determinate:

• qtl - placed between two markers with highest .

• correlation - physical map from cross$maps$physical.

thrRange

Range of the threshold to be checked. Specified in a format(start,stop,step).

cross

An object of class cross. See read.cross for details.

verbose

Be verbose.

Value

None.

Details

This plot is really useful while saturating existing map (using cross.saturate). It helps choose best threshold for marker selection, showing how much markers will be selected with different threshold values.

See Also

• cross.saturate - Saturate existing map.

• reorganizeMarkersWithin - Apply new ordering on the cross object usign ordering vector.

• assignChrToMarkers - Create ordering vector from chromosome assignment vector.

• reduceChromosomesNumber - Number of routines to reduce number of chromosomes of cross object.

• generate.biomarkers - Creating genotype markers out of gene expression data.

Examples

# NOT RUN {
	data(testCross)
	data(testPopulation)
	markerPlacementPlot(testPopulation,placeUsing="qtl",cross=testCross)
	markerPlacementPlot(testPopulation,placeUsing="correlation",cross=testCross)
# }