RFLPtools: Tools to analyse RFLP data

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

Author
Fabienne Flessa, Alexandra Kehl, Mohammed Aslam Imtiaz, Matthias Kohl
Date of publication
2014-08-13 20:17:37
Maintainer
Matthias Kohl <Matthias.Kohl@stamats.de>
License
LGPL-3
Version
1.6

View on R-Forge

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...

Files in this package

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