markerPlacementPlot: Plot number of markers selected.

In KonradZych/phenotypes2genotypes: High-Throughput Generation of Genetic Markers and Maps from Molecular Phenotypes for Crosses Between Inbred Strains

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.

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.

Value

None.

Author(s)

Konrad Zych [e-mail], Danny Arends [e-mail] Maintainer: Konrad Zych [e-mail]

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

	data(testCross)
	data(testPopulation)
	markerPlacementPlot(testPopulation,placeUsing="qtl",cross=testCross)
	markerPlacementPlot(testPopulation,placeUsing="correlation",cross=testCross)

KonradZych/phenotypes2genotypes documentation built on May 30, 2019, 2:45 p.m.