pheno2geno (version 1.4.0)

cross.saturate: Saturate an existing genetic map.

Description

Saturating an existing genetic map using markers derived from phenotype data.

Usage

cross.saturate(population, cross, map=c("genetic","physical"), placeUsing=c("qtl",
  "correlation"), flagged = c("remove","warn","ignore"), threshold=3, chr, env,
  use.orderMarkers=FALSE, verbose=FALSE, debugMode=0)

Arguments

population

An object of class population. See create.population for details.

cross

An object of class cross. See read.cross for details. If not supplied, it will be created using data from the population object

map

Which map should be used for comparison:

• genetic - genetic map from cross$maps$genetic.

• physical - physical map from cross$maps$physical.

placeUsing

How should the position of the new markers on the saturated map be determinated:

• qtl - position the new markers between / next to markers with high LOD score (see threshold).

• correlation - position the new markers on the locations with the highest correction to markers on the physical map from cross$maps$physical.

flagged

How to handle the markers influenced by epistatic or environmental interactions:

• remove - warn about every marker affected and remove them.

• warn - warn about every marker affected but leave them in.

• ignore - leave them in.

threshold

Specifies a threshold for the selection of new phenotype markers (see markerPlacementPlot).

chr

When specified the algorithm only saturates a subset of chromosomes. If not specified, all the chromosomes will be saturated.

env

Vector of environmental conditions - for each of the individuals specifies a condition. Ignored if missing.

use.orderMarkers

If true the algorithm (after initial saturation) performs an orderMarkers on the newly created map.

verbose

Be verbose.

debugMode

Either use 1 or 2, this will modify the amount of information returned to the user. 1) Print out checks, 2) Print additional time information.

Value

An object of class population. See create.population for details.

Details

This function saturates an existing map with markers derived from the phenotype data provided inside either the cross or population object. A correlation matrix between those two sets of markers is made, and new markers are assigned to the 'optimal' location on the map.

See Also

• reorganizeMarkersWithin - Apply new ordering on the cross object usign ordering vector.

• assignChrToMarkers - Create ordering vector from chromosome assignment vector.

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

• reduceChromosomesNumber - Functions to reduce the number of chromosomes in a cross object.

• markerPlacementPlot - Plot showing how many markers will be selected for map saturation with different thresholds.

Examples

# NOT RUN {
	data(testPopulation)
	cross <- cross.saturate(testPopulation,map="genetic",verbose=TRUE,debugMode=2)
# }