Analysis of AFLP data


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Documentation for package ‘AFLP’ version 0.4.0-71

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AFLP-package A package for scoring Amplification Fragment Length Polymorphism (AFLP) data
addOutliers Appends outliers to an AFLP object
addOutliers-method Add 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
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
border<- Adds or overwrites cut-levels
border<--method Adds or overwrites cut-levels
border<--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) information from an AFLP object
fluorescence-method Extracting fluorescence from an AFLP object
fluorescence-methods Extracting fluorescence from an AFLP object
fluorescence<- Adds or overwrites the fluorescence data
fluorescence<--method Adds or overwrites fluorescence data
fluorescence<--methods Adds or overwrites fluorescence data
ggsave.latex Saves a ggplot graphic to a file and creates the code to include it in a LaTeX document.
hclust-method Performs hierarchical clustering
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 observed fluorescence.
outliers Extract outlier information from an AFLP object
outliers-method Extracts outliers
outliers-methods Extracts outliers
princomp-method Principal component analysis
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<- Adds or overwrites quality control samples in an AFLP object.
QC<--method Adds or overwrites quality control samples
QC<--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<- Extracts the quality data of an AFLP object
quality<--method Adds or overwrites quality data
quality<--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
read.fsa Get fluorescence data from fsa files
read.fsa.bins Estimate optimal binning from fsa files
readABI Append fluorescence data from a ABI file to an AFLP object
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<- Adds or overwrites the replicates
replicates<--method Adds or overwrites replicates
replicates<--methods Adds or overwrites replicates
resid-method Extracts the residual outliers
resid-methods Extracts the residual outliers
residuals-method Extracts the residual outliers
residuals-methods Extracts the residual outliers
specimens Extracts the specimen information from an object
specimens-method Methods for extracting specimen information
specimens-methods Methods for extracting specimen information
TiliaDesign Raw AFLP data from Tilia samples
Tilia_bandvaluespc1 Raw AFLP data from Tilia samples
Tilia_bandvaluespc2 Raw AFLP data from Tilia samples
Tilia_bandvaluespc3 Raw AFLP data from Tilia samples
Tilia_bandvaluespc4 Raw AFLP data from Tilia samples