AFLP: Analysis of AFLP data

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.

AuthorThierry Onkelinx, Pieter Verschelde, Sabrina Neirynck, David Halfmaerten, Gerrit Genouw, Paul Quataert
Date of publication2014-04-23 12:21:56
MaintainerThierry Onkelinx <>

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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/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/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

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