RFLPtools (version 2.0)

RFLPtools-package: 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

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

# NOT RUN {
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")
# }