Man pages for pheno2geno
High-Throughput Generation of Genetic Markers and Maps from Molecular Phenotypes for Crosses Between Inbred Strains
| 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. |
