# spgs: Statistical Patterns in Genomic Sequences

A collection of statistical hypothesis tests and other techniques for identifying certain spatial relationships/phenomena in DNA sequences. In particular, it provides tests and graphical methods for determining whether or not DNA sequences comply with Chargaff's second parity rule or exhibit purine-pyrimidine parity. In addition, there are functions for efficiently simulating discrete state space Markov chains and testing arbitrary symbolic sequences of symbols for the presence of first-order Markovianness. Also, it has functions for counting words/k-mers (and cylinder patterns) in arbitrary symbolic sequences. Functions which take a DNA sequence as input can handle sequences stored as SeqFastadna objects from the 'seqinr' package.

- Author
- Andrew Hart [aut, cre], Servet Martnez [aut], Universidad de Chile [cph], INRIA-Chile [cph]
- Date of publication
- 2015-03-28 07:40:29
- Maintainer
- Andrew Hart <ahart@dim.uchile.cl>
- License
- GPL (>= 2)
- Version
- 1.0

## Man pages

- agct.test
- Test of Purine-Pyrimidine Parity Based on Euclidean distance
- ag.test
- Test of Purine-Pyrimidine Parity Based on Purine Count
- array2vector
- Convert Arrays and Tables to Vectors with Named Elements
- chargaff0.test
- Vector Test of Chargaff's Second Parity Rule (CSPR) for...
- chargaff1.test
- Matrix Test of CSPR for Mononucleotides
- chargaff2.test
- Matrix Test of CSPR for Dinucleotides
- chargaff.gibbs.test
- Test of CSPR for Dinucleotides Under Gibbs Distribution
- chisq.unif.test
- Test of Uniformity Based on Pearsons's Chi-Squared test
- complement
- Complement of a DNA/RNA Sequence
- cylinder.counts
- Count Cylinders (Fixed-Offset Patterns) in Character Vectors
- diffsign.test
- the Differents-Sign Test of Statistical Independence
- diid.disturbance
- Construct feasible Random Noise Generating a Bernoulli...
- diid.test
- A Test for a Bernoulli Scheme (IID Sequence)
- disambiguate
- Disambiguate a Nucleic Sequence
- estimateMarkovChain
- Fit a first-Order Markov Chain to a Sequence of Finite...
- ks.unif.test
- Using 'ks.test' to test for Uniformity on the Unit Interval
- lb.test
- The Ljung-Box Test for Uncorrelated Data
- markov.disturbance
- Construct feasible Random Noise Generating a First-Order...
- markov.test
- A Test for First-Order Markovianness
- nanoarchaeum
- DNA sequence for the Nanoarchaeum equitans Kin4-M Chromosome
- oligoProfile
- Oligo Profiles and Oligo Profile Correlation Plots of...
- pair.counts
- Count Pairs in Character Vectors
- pieris
- DNA sequence for the Pieris Rapae Granulovirus Genome
- quadruple.counts
- Count Quadruplets in Character Vectors
- rank.test
- The Rank Test of Statistical Independence
- rcspr2mat
- Random Stochastic Matrices Complying with Chargaff's Second...
- reverseComplement
- Reverse Complement of a DNA/RNA Sequence
- rstochmat
- Random Generation of Stochastic Matrices
- rstochvec
- Random Generation of Stochastic (Probability) Vectors
- simulateMarkovChain
- Simulate a first-Order Markov Chain
- spgs-package
- Statistical Patterns in Genomic Sequences
- triple.counts
- Count Triplets in Character Vectors
- turningpoint.test
- The Turning Point Test of Statistical Independence

## Files in this package

spgs |

spgs/configure.ac |

spgs/tests |

spgs/tests/profileTest.R |

spgs/tests/countingTest.R |

spgs/tests/profileTest.Rout.savefile |

spgs/tests/countingTest.Rout.savefile |

spgs/src |

spgs/src/uint64.h |

spgs/src/sharedef.h |

spgs/src/spgs.h |

spgs/src/spgs.c |

spgs/src/Makevars.in |

spgs/src/Makevars.win |

spgs/NAMESPACE |

spgs/data |

spgs/data/nanoarchaeum.rda |

spgs/data/pieris.rda |

spgs/data/datalist |

spgs/R |

spgs/R/reverseComplement.R |

spgs/R/chargaff1.test.R |

spgs/R/complement.R |

spgs/R/chargaff.gibbs.test.R |

spgs/R/chargaff2.test.R |

spgs/R/sysdata.rda |

spgs/R/profile.R |

spgs/R/randmat.R |

spgs/R/MarkovChains.R |

spgs/R/ag.test.R |

spgs/R/hooks.R |

spgs/R/diid.test.R |

spgs/R/ISPHelpers.R |

spgs/R/markov.test.R |

spgs/R/print.R |

spgs/R/agct.test.R |

spgs/R/counting.R |

spgs/R/oligoCorr.R |

spgs/R/disambiguate.R |

spgs/R/FHatCovariances.R |

spgs/R/GibbsCovariances.R |

spgs/R/chargaff0.test.R |

spgs/R/auxtests.R |

spgs/MD5 |

spgs/DESCRIPTION |

spgs/configure |

spgs/man |

spgs/man/oligoProfile.Rd |

spgs/man/agct.test.Rd |

spgs/man/rank.test.Rd |

spgs/man/simulateMarkovChain.Rd |

spgs/man/rcspr2mat.Rd |

spgs/man/diffsign.test.Rd |

spgs/man/triple.counts.Rd |

spgs/man/turningpoint.test.Rd |

spgs/man/chargaff1.test.Rd |

spgs/man/rstochmat.Rd |

spgs/man/quadruple.counts.Rd |

spgs/man/diid.test.Rd |

spgs/man/complement.Rd |

spgs/man/chargaff0.test.Rd |

spgs/man/disambiguate.Rd |

spgs/man/pieris.Rd |

spgs/man/chisq.unif.test.Rd |

spgs/man/ag.test.Rd |

spgs/man/chargaff2.test.Rd |

spgs/man/ks.unif.test.Rd |

spgs/man/lb.test.Rd |

spgs/man/rstochvec.Rd |

spgs/man/diid.disturbance.Rd |

spgs/man/nanoarchaeum.Rd |

spgs/man/markov.test.Rd |

spgs/man/cylinder.counts.Rd |

spgs/man/reverseComplement.Rd |

spgs/man/markov.disturbance.Rd |

spgs/man/estimateMarkovChain.Rd |

spgs/man/array2vector.Rd |

spgs/man/chargaff.gibbs.test.Rd |

spgs/man/pair.counts.Rd |

spgs/man/spgs-package.Rd |

spgs/cleanup |