Statistical Patterns in Genomic Sequences
Description
provides functions for exploring and testing statistical properties and patterns in DNA sequences.
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 purinepyrimidine 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/kmers and cylinders in symbolic sequences

pair.counts
,triple.counts
,quadruple.counts
,cylinder.counts
The word/kmer 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.
Author(s)
Andrew Hart and Servet Mart<ed>nez
Maintainer: Andrew Hart <ahart@dim.uchile.cl>
References
Hart, A.G. and Mart<ed>nez, S. (2011) Statistical testing of Chargaff's second parity rule in bacterial genome sequences. Stoch. Models 27(2), 1–46.
Hart, A.G. and Mart<ed>nez, S. (2014) Markovianness and Conditional Independence in Annotated Bacterial DNA. Stat. Appl. Genet. Mol. Biol. 13(6), 693716. arXiv:1311.4411 [qbio.QM].
Hart, A.G. and Mart<ed>nez, S. (2012) A Gibbs approach to Chargaff's second parity rule. J. Stat. Phys. 146(2), 408422. arXiv:1105.0685 [math.pr].
See Also
seqinr
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