AFLP: Analysis of AFLP data
Version 0.4.0-71

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 <Thierry.Onkelinx@inbo.be>
LicenseGPL-2
Version0.4.0-71
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("AFLP", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

AFLP-package: A package for scoring Amplification Fragment Length...
fluorescence-set-methods: Adds or overwrites fluorescence data
ggsave.latex: Saves a ggplot graphic to a file and creates the code to...
princomp-methods: Principal component analysis
QC-set: Adds or overwrites quality control samples in an AFLP object.
read.fsa: Get fluorescence data from fsa files
repeatability: Estimate the repeatability of AFLP data
See all...

All man pages Function index File listing

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

Functions

Files

DESCRIPTION
NAMESPACE
R
R/AFLP-outlier.R
R/AFLP-package.R
R/AFLP.R
R/QC.R
R/addOutliers.R
R/as-AFLP.R
R/border.R
R/borderProbability.R
R/classify.R
R/clean.R
R/defineBins.R
R/dummySlabgel.R
R/fluorescence.R
R/ggsave-latex.R
R/hclust.R
R/is-AFLP.R
R/markers.R
R/normalise.R
R/outliers.R
R/princomp.R
R/quality.R
R/randomiseCapilar.R
R/randomiseSlabgel.R
R/rbind-AFLP-outlier.R
R/readABI.R
R/readSAGA.R
R/readfsa.R
R/repeatability.R
R/replicates.R
R/residuals.R
R/specimens.R
build
build/vignette.rds
data
data/Tilia.rda
data/TiliaDesign.rda
data/datalist
inst
inst/doc
inst/doc/AFLP.R
inst/doc/AFLP.Rnw
inst/doc/AFLP.pdf
inst/extdata
inst/extdata/Tilia_bandvaluespc1
inst/extdata/Tilia_bandvaluespc2
inst/extdata/Tilia_bandvaluespc3
inst/extdata/Tilia_bandvaluespc4
man
man/AFLP-class.Rd
man/AFLP-package.Rd
man/AFLP.Rd
man/AFLP.outlier-class.Rd
man/AFLP.outlier.Rd
man/QC-method.Rd
man/QC-set-methods.Rd
man/QC-set.Rd
man/QC.Rd
man/TiliaDesign.Rd
man/addOutliers-methods.Rd
man/addOutliers.Rd
man/as.AFLP.Rd
man/border-method.Rd
man/border-set-methods.Rd
man/border-set.Rd
man/border.Rd
man/borderProbability.Rd
man/classify.Rd
man/clean.Rd
man/defineBins.Rd
man/dummySlabgel.Rd
man/fluorescence-methods.Rd
man/fluorescence-set-methods.Rd
man/fluorescence-set.Rd
man/fluorescence.Rd
man/ggsave.latex.Rd
man/hclust-methods.Rd
man/is.AFLP.Rd
man/markers-method.Rd
man/markers.Rd
man/normalise.Rd
man/outliers-methods.Rd
man/outliers.Rd
man/princomp-methods.Rd
man/quality-method.Rd
man/quality-set-methods.Rd
man/quality-set.Rd
man/quality.Rd
man/randomiseCapilar.Rd
man/randomiseSlabgel.Rd
man/rbind.AFLP.outlier.Rd
man/read.fsa.Rd
man/read.fsa.bins.Rd
man/readABI.Rd
man/readSAGA.Rd
man/repeatability.Rd
man/replicates-method.Rd
man/replicates-set-methods.Rd
man/replicates-set.Rd
man/replicates.Rd
man/resid-methods.Rd
man/residuals-methods.Rd
man/specimens-methods.Rd
man/specimens.Rd
vignettes
vignettes/AFLP.Rnw
AFLP documentation built on May 21, 2017, 3:46 a.m.

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