pheno2geno (version 1.4.0)

modify number of chromosomes: Change the number of chromosomes in a cross object

Description

Methods to manually modify the number of chromosomes inside an cross object

Usage

reduceChromosomesNumber(cross, numberOfChromosomes, verbose=FALSE)
    removeChromosomes(cross, chromosomesToBeRmv, verbose=FALSE)
    removeTooSmallChromosomes(cross, minNrOfMarkers, verbose=FALSE)

Arguments

cross

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

numberOfChromosomes

How many chromosomes should stay (remove all but 1:numberOfChromosomes).

chromosomesToBeRmv

NAMES of chromosomes to be removed.

minNrOfMarkers

Specify minimal number of markers chromosome is allowed to have (remove all that have less markers than that).

verbose

Be verbose.

Value

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

Details

There are three functions in pheno2geno to allow the user to manually reduce number of resulting chromosomes.

reduceChromosomesNumber This functions removes all chromosomes from the cross object excluding chromosome 1 to numberOfChromosomes. It depends on the ordering of chromosomes inside the cross object (which is based on the length of the chromosomes).

removeChromosomes This function removes chromosomes from the cross object by name. Because of this it does not depend on the ordering of the chromosomes inside the cross object.

removeTooSmallChromosomes This function is used to clean a cross object after using formLinkageGroups. FormLinkageGroups can introduce small chromosomes as artifacts. These linkage groups consist of only a few markers with poor quality and should be removed from the cross object.

See Also

reorganizeMarkersWithin - Apply new ordering on the cross object usign ordering vector. assignChrToMarkers - Create ordering vector from chromosome assignment vector. cross.saturate - Saturate existing map. cross.denovo - Create de novo genetic map.

Examples

# NOT RUN {
    data(testCross)
    plotRF(testCross, main="riself generate.biomarkers example")
    cross_ <- reduceChromosomesNumber(testCross,5,verb=TRUE)
    plotRF(cross_, main="Leaving only 5 chromosomes")
    cross_ <- removeChromosomes(testCross,1,verb=TRUE)
    plotRF(cross_, main="Removing chromosome 1")
    cross_ <- removeTooSmallChromosomes(testCross,5,verb=TRUE)
    plotRF(cross_, main="Leaving only chromosomes with more than 5 markers")
# }