RFLPtools: Tools to analyse RFLP data
Version 1.6

RFLPtools provides functions to analyse DNA fragment samples (i.e. derived from RFLP-analysis) and standalone BLAST report files (i.e. DNA sequence analysis).

Browse man pages Browse package API and functions Browse package files

AuthorFabienne Flessa, Alexandra Kehl, Mohammed Aslam Imtiaz, Matthias Kohl
Date of publication2014-08-14 00:46:05
MaintainerMatthias Kohl <Matthias.Kohl@stamats.de>
LicenseLGPL-3
Version1.6
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RFLPtools")

Man pages

0RFLP-package: Tools to analyse RFLP-data
BLASTdata: Example data set for BLAST data
diffDist: Distance Matrix Computation
FragMatch: Compute matches for RFLP data via FragMatch.
germ: Compute matches for RFLP data via GERM.
linCombDist: Linear Combination of Distances
newDataGerm: Example data set from GERM software
nrBands: Function to compute number of bands.
read.blast: Read BLAST data
read.rflp: Read RFLP data
refDataGerm: Example data set from GERM software
RFLPcombine: Combine RFLP data sets
RFLPdata: Example data set for RFLP data
RFLPdist: Compute distances for RFLP data.
RFLPdist2: Compute distances for RFLP data.
RFLPdist2ref: Compute distance between RFLP data and RFLP reference data.
RFLPlod: Remove bands below LOD
RFLPplot: Function to plot RFLP data.
RFLPqc: Quality control for RFLP data
RFLPref: Example data set for RFLP reference
RFLPrefplot: Function for a visual comparison of RFLP samples with...
sim2dist: Convert similarity matrix to dist object.
simMatrix: Similarity matrix for BLAST data.
simulateRFLPdata: Simulate RFLP data.
write.hclust: Cut a hierarchical cluster tree and write cluster identifiers...

Functions

BLASTdata Man page
FragMatch Man page Source code
RFLPcombine Man page Source code
RFLPdata Man page
RFLPdist Man page Source code
RFLPdist2 Man page Source code
RFLPdist2ref Man page Source code
RFLPlod Man page Source code
RFLPplot Man page Source code
RFLPqc Man page Source code
RFLPref Man page
RFLPrefplot Man page Source code
RFLPtools Man page
RFLPtools-package Man page
backward Source code
countMatches Source code
diffDist Man page Source code
forward Source code
germ Man page Source code
linCombDist Man page Source code
newDataGerm Man page
nrBands Man page Source code
read.blast Man page Source code
read.rflp Man page Source code
refDataGerm Man page
sim2dist Man page Source code
simMatrix Man page Source code
simulateRFLPdata Man page Source code
write.hclust Man page Source code

Files

inst
inst/CITATION
inst/scripts
inst/scripts/SimulationStudy.R
inst/extdata
inst/extdata/BLASTexample.txt
inst/extdata/AZ091016_report.txt
inst/extdata/RFLPexample.txt
inst/doc
inst/doc/RFLPtools.pdf
inst/doc/RFLPtools.Rnw
inst/doc/RFLPtools.R
NAMESPACE
NEWS
data
data/refDataGerm.RData
data/RFLPdata.RData
data/BLASTdata.RData
data/newDataGerm.RData
data/RFLPref.RData
R
R/RFLPrefplot.R
R/RFLPdist2.R
R/RFLPqc.R
R/read.rflp.R
R/RFLPlod.R
R/FragMatch.R
R/RFLPdist.R
R/germ.R
R/read.blast.R
R/linCombDist.R
R/simulateRFLPData.R
R/simMatrix.R
R/sim2dist.R
R/RFLPplot.R
R/write.hclust.R
R/RFLPcombine.R
R/diffDist.R
R/RFLPdist2ref.R
vignettes
vignettes/logoUBT.png
vignettes/HFU.jpg
vignettes/RFLPtools.Rnw
vignettes/logoTueb.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/simMatrix.Rd
man/linCombDist.Rd
man/newDataGerm.Rd
man/RFLPdata.Rd
man/sim2dist.Rd
man/RFLPdist2.Rd
man/RFLPrefplot.Rd
man/RFLPqc.Rd
man/RFLPplot.Rd
man/0RFLP-package.Rd
man/simulateRFLPdata.Rd
man/write.hclust.Rd
man/RFLPlod.Rd
man/RFLPcombine.Rd
man/RFLPdist2ref.Rd
man/germ.Rd
man/read.blast.Rd
man/nrBands.Rd
man/RFLPref.Rd
man/BLASTdata.Rd
man/read.rflp.Rd
man/diffDist.Rd
man/RFLPdist.Rd
man/refDataGerm.Rd
man/FragMatch.Rd
RFLPtools documentation built on May 20, 2017, 12:06 a.m.