markersCorPlot: Plotting correlation between markers on two maps.

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

Description

Plotting correlation between two maps together with markers placement (comparison of coverage).

Usage

  markersCorPlot(cross, population, map=c("genetic","physical"), cmBetween=25,
    comparisonMethod = c(sumMajorityCorrelation,majorityCorrelation,
    meanCorrelation,majorityOfMarkers), chr, show.legend=FALSE, verbose=TRUE)

Arguments

cross	R/qtl cross type object.
population	An object of class population.
map	Which map (from ones stored in population$maps) should be used fo assigning chromosomes on the created map.
cmBetween	Offset between chromosomes specified in cM.
comparisonMethod	Method used to compare chromosomes from the new map to the original ones while assigning: sumMajorityCorrelation - For each chromosome in cross for every marker checks the marker it is having highest correlation with. Checks on which chromosome this marker is placed in old map. For each of new chromosomes one or more of chromosomes from old map will be represented. Function sums correlations for each pair of those and for every new chromosomes assigns old chromosome with highest cumulative cor. majorityCorrelation - For each chromosome in cross for every marker checks the marker it is having highest correlation with. Checks on which chromosome this marker is placed in old map. For each of new chromosomee, old chromosome with most markers with high correlation is assigned. meanCorrelation - Assigning chromosome from new map to old ones using sum of the mean correlation between their markers. majorityOfMarkers - For each chromosome in the cross object (either created inside the function or provided by user) chromosome from original map, where most markers from new chromosome are is assigned.
chr	Specifies subset of chromosomes to be shown.
show.legend	Shall the legend be shown on the plot.
verbose	Be verbose.

Details

Plots markers from moth old and new map as points and in the background - comparison between them done using selected comparison method.

Value

Matrix of comparisons between chromosomes obtained using comparison method.

Author(s)

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

See Also

• plotMapComparison - Plotting routine for comparison of two genetic maps.

• projectOldMarkers - Plotting routine for showing how markers from original map are placed on saturated map.

• cross.saturate - Saturate existing map.

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

Examples

	data(testPopulation)
	data(testCross)
	markersCorPlot(testCross,testPopulation,map="genetic")

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