assignedChrToMarkers: Function that assigns a chromosome label to a genetic marker

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

Description

This functions returns an ordering vector of markers for each marker it shows which chromosome the marker belongs to.

Usage

	assignChrToMarkers(assignment, cross)

Arguments

assignment	Chromosome assignment vector created using cross.denovo with reOrder = FALSE
cross	An object of class cross. See read.cross for details.

Details

When using the cross.denovo function with the parameter reOrder = FALSE, its return value will be a chromosome assignment vector. This chromosome assignment vector shows how chromosomes from the created map are assigned to chromosomes from the original map. By using the assignChrToMarkers function the chromosome assignment vector is transformed into a marker ordering vector, which is used by reorganizeMarkersWithin to reorder markers inside the cross object.

Value

Ordering vector, that can be used by reorganizeMarkersWithin function to reorder the cross object.

Author(s)

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

See Also

reorganizeMarkersWithin - Apply new ordering on the cross object using ordering vector. cross.saturate - Saturate existing map. cross.denovo - Create de novo genetic map or vector showing how chromosomes should be assigned.

Examples

	data(testCross)
	data(testPopulation)
	assignment <- cross.denovo(testPopulation,n.chr=5,verbose=TRUE,map="genetic",
  comparisonMethod=sumMajorityCorrelation, use.orderMarkers=FALSE,reOrder=FALSE)
  assignment
  ordering <- assignChrToMarkers(assignment,testCross)

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