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 <Thierry.Onkelinx@inbo.be>
LicenseGPL-2
Version0.4.0-71

View on R-Forge

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

addOutliers Man page
addOutliers,AFLP,AFLP.outlier-method Man page
addOutliers,AFLP,data.frame-method Man page
addOutliers-methods Man page
AFLP Man page
AFLP-class Man page
AFLP.outlier Man page
AFLP.outlier-class Man page
AFLP-package Man page
as.AFLP Man page
border Man page
border<- Man page
border<-,AFLP-method Man page
border,AFLP-method Man page
border-method Man page
border<--methods Man page
borderProbability Man page
classify Man page
clean Man page
defineBins Man page
dummySlabgel Man page
fluorescence Man page
fluorescence<- Man page
fluorescence<-,AFLP,data.frame-method Man page
fluorescence,AFLP-method Man page
fluorescence<--methods Man page
fluorescence-methods Man page
ggsave.latex Man page
hclust,AFLP-method Man page
hclust-methods Man page
is.AFLP Man page
markers Man page
markers,AFLP.outlier-method Man page
markers-method Man page
normalise Man page
outliers Man page
outliers,AFLP-method Man page
outliers-methods Man page
princomp,AFLP-method Man page
princomp-methods Man page
QC Man page
QC<- Man page
QC<-,AFLP-method Man page
QC,AFLP-method Man page
QC-method Man page
QC<--methods Man page
quality Man page
quality<- Man page
quality<-,AFLP-method Man page
quality,AFLP-method Man page
quality-method Man page
quality<--methods Man page
randomiseCapilar Man page
randomiseSlabgel Man page
rbind.AFLP.outlier Man page
readABI Man page
read.fsa Man page
read.fsa.bins Man page
readSAGA Man page
repeatability Man page
replicates Man page
replicates<- Man page
replicates<-,AFLP-method Man page
replicates,AFLP-method Man page
replicates,AFLP.outlier-method Man page
replicates-method Man page
replicates<--methods Man page
resid,AFLP.outlier-method Man page
resid-methods Man page
residuals,AFLP.outlier-method Man page
residuals-methods Man page
specimens Man page
specimens,AFLP-method Man page
specimens,AFLP.outlier-method Man page
specimens-methods Man page
Tilia_bandvaluespc1 Man page
Tilia_bandvaluespc2 Man page
Tilia_bandvaluespc3 Man page
Tilia_bandvaluespc4 Man page
TiliaDesign Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.