spgs-package: tools:::Rd_package_title("spgs")

Description

provides functions for exploring and testing statistical properties and patterns in DNA sequences.

Arguments

Author

Andrew Hart and Servet Martínez

Maintainer: tools:::Rd_package_maintainer("spgs")

Details

Package:	spgs
Type:	Package
License:	GPL (>= 2)

This package provides a range of statistical tests for various properties of DNA and/or other genomic sequences. There are eight groups of functions:

Testing for Chargaff's second parity rule in bacteria and other DNA sequences: chargaff0.test, chargaff1.test, chargaff2.test, chargaff.gibbs.test, oligoProfile
Testing for purine-pyrimidine parity in viruses and other DNA sequences: ag.test, agct.test
Testing for Bernoulli/Markov processes: markov.test, diid.test
Independence tests: diffsign.test, turningpoint.test, rank.test, lb.test
Tests for uniform distribution: ks.unif.test, chisq.unif.test
Simulation of random vectors, stochastic matrices, Bernoulli processes and Markov chains: simulateMarkovChain, estimateMarkovChain, rstochvec, rstochmat, rcspr2mat
Functions for obtaining the complement or reverse complement of a DNA sequence: complement, reverseComplement
Functions for counting words/k-mers and cylinders in symbolic sequences: pair.counts, triple.counts, quadruple.counts, cylinder.counts

The word/k-mer counting functions are general and can deal with arbitrary symbolic sequences, not only DNA sequences.

Functions which take a DNA sequence as input are able to work with sequences stored as SeqFastadna objects generated by the seqinr package.

References

Hart, A.G. and Martínez, S. (2011) Statistical testing of Chargaff's second parity rule in bacterial genome sequences. Stoch. Models 27(2), 1--46.

Hart, A.G. and Martínez, S. (2014) Markovianness and Conditional Independence in Annotated Bacterial DNA. Stat. Appl. Genet. Mol. Biol. 13(6), 693-716. arXiv:1311.4411 [q-bio.QM].

Hart, A.G. and Martínez, S. (2012) A Gibbs approach to Chargaff's second parity rule. J. Stat. Phys. 146(2), 408-422. arXiv:1105.0685 [math.pr].