save.gff: Saving gff files.

In pheno2geno: High-Throughput Generation of Genetic Markers and Maps from Molecular Phenotypes for Crosses Between Inbred Strains

Description

Saving gff files.

Usage

save.gff(cross, map.physical, ind, gffFileCore="population", verbose=FALSE)

Arguments

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.physical	Map with physical locations of the markers. A matrix with three columns - chromosome/ start position/ end position. Just like physical map in population object, see: read.population
ind	Which individuals should be saved. Numeric vector. If missing - all individuals will be selected.
gffFileCore	Name of the gff files core. For each of the individuals a separated file is created with a name: "core" +"ind_x.gff".
verbose	Be verbose.

Details

This function saves gff files, that can be visualised using most of the genome viewers. The files contain physical location of markers and recombination breakpoints. Therefore, physical map should be stored in an object of class population. Redundant markers are the markers having the same loaction on the genomic map, but different on the physical map. These may be produced e.g. by cross.saturate function (markers that have QTL exactly on the position where an original marker is located). Also, as a result of smoothing genotypping errors some markers may be put on the same position on the genetic map.

Value

None.

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 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

	data(testPopulation)
	cross <- cross.saturate(testPopulation,map="genetic",verbose=TRUE,debugMode=2)

pheno2geno documentation built on May 2, 2019, 6:35 a.m.