pheno2geno (version 1.4.0)

reorganizeMarkersWithin: Reorganize markers within cross object.

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.

Value

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

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.

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

# NOT RUN {
  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)

# }