reorganizeMarkersWithin: Reorganize markers within cross object.

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

Description

Reorder markers within cross object using supplied marker ordering vector.

Usage

  reorganizeMarkersWithin(cross, ordering)

Arguments

cross	An object of class cross. See read.cross for details.
ordering	Ordering vector specifying for every marker in the cross object (by name) which new chromosome this marker will be moved to.

Details

Functions reorders an object of class cross using the supplied marker ordering vector. This vector contains for each marker the chromosome number that this marker will be moved to.

Value

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

Author(s)

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

See Also

• cross.denovo - Creating a de novo genetic map or a chromosome assignment vector.

• cross.saturate - Saturate an existing genetic map by using phenotype markers.

• assignChrToMarkers - Create ordering vector from chromosome assignment vector.

Examples

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

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