add.to.population | Add additional data to a population object |
assignedChrToMarkers | Function that assigns a chromosome label to a genetic marker |
changeChromNumber | Change the number of chromosomes in a cross object |
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. |
fake.population | Simulate a population object. |
findDiffExpressed | Finding differentially expressed genes. |
find.mixups | Find sample mix-ups |
generate.biomarkers | Generate discrete biomarkers from the continuous phenotypes |
map.functions | Functions to provide some descriptive statistics on genetic... |
markerPlacementPlot | Plot number of markers selected. |
markersCorPlot | Plotting correlation between markers on two maps. |
phenotypes2genotypes-internal | Internal pheno2geno functions |
phenotypes2genotypes-package | Pheno2Geno - High-throughput generation of genetic markers... |
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. |
power.plot | Comparison of power of qtl detection. |
projectOldMarkers | Plotting routine which shows where markers from original map... |
pull.biomarkers | Extract the detected biomarkers from a population object. |
qtl.comparison.plot | Comparison of qtl profiles. |
read.population | Loading genotype and phenotype data |
reorganizeMarkersWithin | Reorganize markers within cross object. |
RPpval | Visualize the outcome of a Rank product analysis |
save.gff | Saving gff files. |
scan.qtls | Scan qtls |
set.geno.from.cross | Pull genotype from an object of class cross. |
testCross | Test cross object |
testPopulation | Test population object |
transformations | Basic functions to do transformation / normalization of... |
write.population | Writes a population object to file. |
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