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

## Documentation for package ‘pheno2geno’ version 1.3.1

- DESCRIPTION file.

## Help Pages

add.to.population | Add additional data to a population object
add.to.populationSub.internal | Add additional data to a population object
assignChrToMarkers | Function that assigns a chromosome label to a genetic marker
assignMaximum | Create a de novo genetic map from a population object.
assignMaximumNoConflicts | Create a de novo genetic map from a population object.
avg_map_distances | Functions to provide some descriptive statistics on genetic maps
coloringMode | Plotting routine for comparison of two genetic maps.
create.population | Create a population object
cross.denovo | Create a de novo genetic map from a population object.
cross.saturate | Saturate an existing genetic map.
dataObject | Add additional data to a population object
dataType | Add additional data to a population object
fake.population | Simulate a population object.
find.diff.expressed | Finding differentially expressed genes.
find.mixups | Find sample mix-ups
generate.biomarkers | Generate discrete biomarkers from the continuous phenotypes
groupLabels | Finding differentially expressed genes.
logarithmic | plotMarkerDistribution
majorityCorrelation | Create a de novo genetic map from a population object.
majorityOfMarkers | Create a de novo genetic map from a population object.
map_distances | Functions to provide some descriptive statistics on genetic maps
margin | Generate discrete biomarkers from the continuous phenotypes
markerPlacementPlot | Plot number of markers selected.
markers | Plotting routine for children expression data.
markersCorPlot | Plotting correlation between markers on two maps.
meanCorrelation | Create a de novo genetic map from a population object.
overlapInd | Generate discrete biomarkers from the continuous phenotypes
pheno2geno | Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes
phenotypeRow | plotMarkerDistribution
plotChildrenExpression | Plotting routine for children expression data.
plotMapComparison | Plotting routine for comparison of two genetic maps.
plotMarkerDistribution | plotMarkerDistribution
plotParentalExpression | Plotting routine for parental expression data.
plotRPpval | Visualize the outcome of a Rank product analysis
population | Create a population object
power.plot | Comparison of power of qtl detection.
projectOldMarkers | Plotting routine which shows where markers from original map are located on saturated map.
proportion | Generate discrete biomarkers from the continuous phenotypes
pull.biomarkers | Extract the detected biomarkers from a population object.
qtl.comparison.plot | Comparison of qtl profiles.
read.population | Loading genotype and phenotype data
reduceChromosomesNumber | Change the number of chromosomes in a cross object
removeChromosomes | Change the number of chromosomes in a cross object
removeTooSmallChromosomes | Change the number of chromosomes in a cross object
reorganizeMarkersWithin | Reorganize markers within cross object.
save.gff | Saving gff files.
scan.qtls | Scan qtls
set.geno.from.cross | Pull genotype from an object of class cross.
showRPpval | Visualize the outcome of a Rank product analysis
sumMajorityCorrelation | Create a de novo genetic map from a population object.
testCross | Test cross object
testPopulation | Test population object
transformation | Basic functions to do transformation / normalization of phenotypes.
write.population | Writes a population object to file.