Tools to Analyse RFLP Data
Provides functions to analyse DNA fragment samples (i.e. derived from RFLP-analysis) and standalone BLAST report files (i.e. DNA sequence analysis).
News
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NEWS to package RFLPtools
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Version 1.6
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- added reference Flessa et al. (2013) to man files.
- added some further checks for function input.
- functions RFLPdist and RFLPdist2ref obtained an argument LOD for handling
values below some given limit of detection (LOD).
- new example datasets refDataGerm and newDataGerm taken from the GERM
software
- added function germ which represents an implementation of the Good-Enough
RFLP Matcher (GERM) program.
- added function FragMatch which represents an implementation of the FragMatch
program.
- added function simulateRFLPdata to simulate RFLP data.
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Version 1.5
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- update of vignette
- extension of function RFLPdist2: additional option that missing bands
occur only below a specified LOD
- new function RFLPcombine to combine RFLP datasets
- new function RFLPlod to remove bands below a given limit LOD
- more flexible arguments for functions RFLPplot and RFLPrefplot
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Version 1.4
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- correction of some minor bugs
- added function linCombDist to compute a linear combination of distances
- introduced vignettes folder
- updated affiliations in vignette and added some explanations regarding the
use of NCBI BLAST
- added option "sep" to function "read.blast".
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Version 1.3
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- added function diffDist for distance matrix computation based on
successive differences
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Version 1.2
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- RFLPplot and RFLPrefplot gained argument "colBands" to specify color(s) for
the plotted bands.
- added reference to recent article
- in examples now use of simPlot instead of corPlot, hence requires package
MKmisc version 0.8
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Version 1.1
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- added NEWS file
- some examples simplyfied to reduce check-time
- added warnings for BLAST datasets for the case that there are subject.ids
which do not occur as query.ids
- extended vignette and package Rd-file by RFLPplot and RFLPrefplot examples
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Version 1.0
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- start of implementation, first version on CRAN