Man pages for AFLP
Analysis of AFLP data
| addOutliers | Appends outliers to an AFLP object |
| addOutliers-methods | Add outliers to an AFLP object |
| AFLP | Create an object of the class AFLP |
| AFLP-class | Class "AFLP" |
| AFLP.outlier | Creates an AFLP outlier object |
| AFLP.outlier-class | Outliers of an AFLP object |
| AFLP-package | A package for scoring Amplification Fragment Length... |
| as.AFLP | Convert an object to a AFLP object |
| border | Extracts the cut-levels of an AFLP object |
| border-method | Extract the cut-levels from an AFLP object |
| borderProbability | Internal functions of the AFLP package. |
| border-set | Adds or overwrites cut-levels |
| border-set-methods | Adds or overwrites cut-levels |
| classify | Classifies normalised AFLP data |
| clean | Does some rudimentary cleaning of an AFLP object. |
| defineBins | Define bins in AFLP object |
| dummySlabgel | Simulate some data for a slab gel. |
| fluorescence | Extract the fluorescence (raw, normalised and scored)... |
| fluorescence-methods | Extracting fluorescence from an AFLP object |
| fluorescence-set | Adds or overwrites the fluorescence data |
| fluorescence-set-methods | Adds or overwrites fluorescence data |
| ggsave.latex | Saves a ggplot graphic to a file and creates the code to... |
| hclust-methods | Performs hierarchical clustering |
| is.AFLP | Checks if an object is of the AFLP class |
| markers | Extract the marker information from an object |
| markers-method | Extract the marker information from an object |
| normalise | Perform a normalisation (calibration) procedure on the... |
| outliers | Extract outlier information from an AFLP object |
| outliers-methods | Extracts outliers |
| princomp-methods | Principal component analysis |
| QC | Extracts the quality control samples of an AFLP object |
| QC-method | Extracts the quality control samples of an AFLP object |
| QC-set | Adds or overwrites quality control samples in an AFLP object. |
| QC-set-methods | Adds or overwrites quality control samples |
| quality | Extract the quality data from an AFLP object |
| quality-method | Extract the quality data from an AFLP object |
| quality-set | Extracts the quality data of an AFLP object |
| quality-set-methods | Adds or overwrites quality data |
| randomiseCapilar | Randomise specimens over different capilar AFLP plates. |
| randomiseSlabgel | Randomise specimens over different slab gels. |
| rbind.AFLP.outlier | Combine the information of several AFLP.outlier objects |
| readABI | Append fluorescence data from a ABI file to an AFLP object |
| read.fsa | Get fluorescence data from fsa files |
| read.fsa.bins | Estimate optimal binning from fsa files |
| readSAGA | Append fluorescence data from a SAGA file to an AFLP object |
| repeatability | Estimate the repeatability of AFLP data |
| replicates | Extract the replicates from an object |
| replicates-method | Extract replicates from an object |
| replicates-set | Adds or overwrites the replicates |
| replicates-set-methods | Adds or overwrites replicates |
| resid-methods | Extracts the residual outliers |
| residuals-methods | Extracts the residual outliers |
| specimens | Extracts the specimen information from an object |
| specimens-methods | Methods for extracting specimen information |
| TiliaDesign | Raw AFLP data from Tilia samples |
