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. |