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

Reference manual

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install.packages("RFLPtools")

1.9 by Matthias Kohl, 14 days ago


Browse source code at https://github.com/cran/RFLPtools


Authors: Fabienne Flessa [aut] , Alexandra Kehl [aut] , Mohammed Aslam Imtiaz [aut] , Matthias Kohl [aut, cre]


Documentation:   PDF Manual  


LGPL-3 license


Imports stats, utils, graphics, grDevices

Depends on RColorBrewer

Suggests knitr, rmarkdown, lattice, MKomics


See at CRAN