AFLP: Analysis of AFLP data

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This package assists the analysis of amplified fragment length polymorphism (AFLP) DNA fingerprinting. It has function to randomise samples, calibrate the fluoresences pattern, score the calibrated patterns and do some basic analysis on the scored patterns.

Author
Thierry Onkelinx, Pieter Verschelde, Sabrina Neirynck, David Halfmaerten, Gerrit Genouw, Paul Quataert
Date of publication
2014-04-23 12:21:56
Maintainer
Thierry Onkelinx <Thierry.Onkelinx@inbo.be>
License
GPL-2
Version
0.4.0-71

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Man pages

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

Files in this package

AFLP/DESCRIPTION
AFLP/NAMESPACE
AFLP/R
AFLP/R/AFLP-outlier.R
AFLP/R/AFLP-package.R
AFLP/R/AFLP.R
AFLP/R/QC.R
AFLP/R/addOutliers.R
AFLP/R/as-AFLP.R
AFLP/R/border.R
AFLP/R/borderProbability.R
AFLP/R/classify.R
AFLP/R/clean.R
AFLP/R/defineBins.R
AFLP/R/dummySlabgel.R
AFLP/R/fluorescence.R
AFLP/R/ggsave-latex.R
AFLP/R/hclust.R
AFLP/R/is-AFLP.R
AFLP/R/markers.R
AFLP/R/normalise.R
AFLP/R/outliers.R
AFLP/R/princomp.R
AFLP/R/quality.R
AFLP/R/randomiseCapilar.R
AFLP/R/randomiseSlabgel.R
AFLP/R/rbind-AFLP-outlier.R
AFLP/R/readABI.R
AFLP/R/readSAGA.R
AFLP/R/readfsa.R
AFLP/R/repeatability.R
AFLP/R/replicates.R
AFLP/R/residuals.R
AFLP/R/specimens.R
AFLP/build
AFLP/build/vignette.rds
AFLP/data
AFLP/data/Tilia.rda
AFLP/data/TiliaDesign.rda
AFLP/data/datalist
AFLP/inst
AFLP/inst/doc
AFLP/inst/doc/AFLP.R
AFLP/inst/doc/AFLP.Rnw
AFLP/inst/doc/AFLP.pdf
AFLP/inst/extdata
AFLP/inst/extdata/Tilia_bandvaluespc1
AFLP/inst/extdata/Tilia_bandvaluespc2
AFLP/inst/extdata/Tilia_bandvaluespc3
AFLP/inst/extdata/Tilia_bandvaluespc4
AFLP/man
AFLP/man/AFLP-class.Rd
AFLP/man/AFLP-package.Rd
AFLP/man/AFLP.Rd
AFLP/man/AFLP.outlier-class.Rd
AFLP/man/AFLP.outlier.Rd
AFLP/man/QC-method.Rd
AFLP/man/QC-set-methods.Rd
AFLP/man/QC-set.Rd
AFLP/man/QC.Rd
AFLP/man/TiliaDesign.Rd
AFLP/man/addOutliers-methods.Rd
AFLP/man/addOutliers.Rd
AFLP/man/as.AFLP.Rd
AFLP/man/border-method.Rd
AFLP/man/border-set-methods.Rd
AFLP/man/border-set.Rd
AFLP/man/border.Rd
AFLP/man/borderProbability.Rd
AFLP/man/classify.Rd
AFLP/man/clean.Rd
AFLP/man/defineBins.Rd
AFLP/man/dummySlabgel.Rd
AFLP/man/fluorescence-methods.Rd
AFLP/man/fluorescence-set-methods.Rd
AFLP/man/fluorescence-set.Rd
AFLP/man/fluorescence.Rd
AFLP/man/ggsave.latex.Rd
AFLP/man/hclust-methods.Rd
AFLP/man/is.AFLP.Rd
AFLP/man/markers-method.Rd
AFLP/man/markers.Rd
AFLP/man/normalise.Rd
AFLP/man/outliers-methods.Rd
AFLP/man/outliers.Rd
AFLP/man/princomp-methods.Rd
AFLP/man/quality-method.Rd
AFLP/man/quality-set-methods.Rd
AFLP/man/quality-set.Rd
AFLP/man/quality.Rd
AFLP/man/randomiseCapilar.Rd
AFLP/man/randomiseSlabgel.Rd
AFLP/man/rbind.AFLP.outlier.Rd
AFLP/man/read.fsa.Rd
AFLP/man/read.fsa.bins.Rd
AFLP/man/readABI.Rd
AFLP/man/readSAGA.Rd
AFLP/man/repeatability.Rd
AFLP/man/replicates-method.Rd
AFLP/man/replicates-set-methods.Rd
AFLP/man/replicates-set.Rd
AFLP/man/replicates.Rd
AFLP/man/resid-methods.Rd
AFLP/man/residuals-methods.Rd
AFLP/man/specimens-methods.Rd
AFLP/man/specimens.Rd
AFLP/vignettes
AFLP/vignettes/AFLP.Rnw