| RFLPtools-package {RFLPtools} | R Documentation |
Tools To Analyse RFLP-Data
Description
RFLPtools provides functions to analyse DNA fragment samples (i.e. derived from RFLP-analysis) and standalone BLAST report files (i.e. DNA sequence analysis).
Details
| Package: | RFLPtools |
| Version: | 2.0 |
| Date: | 2022-02-07 |
| Depends: | R(>= 4.0.0) |
| Imports: | stats, utils, graphics, grDevices, RColorBrewer |
| Suggests: | knitr, rmarkdown, lattice, MKomics |
| License: | LGPL-3 |
Author(s)
Fabienne Flessa Fabienne.Flessa@uni-bayreuth.de,
Alexandra Kehl Alexandra.Kehl@uni-tuebingen.de,
Mohammed Aslam Imtiaz,
Matthias Kohl Matthias.Kohl@stamats.de
Maintainer: Matthias Kohl Matthias.Kohl@stamats.de
References
Local Blast download: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
Blast News: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews
Ian A. Dickie, Peter G. Avis, David J. McLaughlin, Peter B. Reich. Good-Enough RFLP Matcher (GERM) program. Mycorrhiza 2003, 13:171-172.
Flessa, F., Kehl, A., Kohl, M. Analysing diversity and community structures using PCR-RFLP: a new software application. Molecular Ecology Resources 2013 Jul; 13(4):726-33.
Matsumoto, Masaru; Furuya, Naruto; Takanami, Yoichi; Matsuyama, Nobuaki. RFLP analysis of the PCR-amplified 28S rDNA in Rhizoctonia solani. Mycoscience 1996 37:351-356.
Persoh, D., Melcher, M., Flessa, F., Rambold, G.: First fungal community analyses of endophytic ascomycetes associated with Viscum album ssp. austriacum and itshost Pinus sylvestris. Fungal Biology 2010 Jul;114(7):585-96.
Poussier, Stephane; Trigalet-Demery, Danielle; Vandewalle, Peggy; Goffinet, Bruno; Luisetti, Jacques; Trigalet, Andre. Genetic diversity of Ralstonia solanacearum as assessed by PCR-RFLP of the hrp gene region, AFLP and 16S rRNA sequence analysis, and identification of an African subdivision. Microbiology 2000 146:1679-1692.
T. A. Saari, S. K. Saari, C. D. Campbell, I. J Alexander, I. C. Anderson. FragMatch - a program for the analysis of DNA fragment data. Mycorrhiza 2007, 17:133-136
Examples
data(RFLPdata)
res <- RFLPdist(RFLPdata)
plot(hclust(res[[1]]), main = "Euclidean distance")
par(mfrow = c(1,2))
plot(hclust(RFLPdist(RFLPdata, nrBands = 3)), cex = 0.7)
RFLPplot(RFLPdata, nrBands = 3, mar.bottom = 6, cex.axis = 0.8)
data(RFLPref)
RFLPrefplot(RFLPdata, RFLPref, nrBands = 6, cex.axis = 0.8)
library(MKomics)
data(BLASTdata)
res <- simMatrix(BLASTdata, sequence.range = TRUE, Min = 500)
myCol <- colorRampPalette(brewer.pal(8, "RdYlGn"))(128)
simPlot(res, col = myCol, minVal = 0,
labels = colnames(res), title = "(Dis-)Similarity Plot")