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 |

**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

agct.test | Man page |

ag.test | Man page |

array2vector | Man page |

chargaff0.test | Man page |

chargaff1.test | Man page |

chargaff2.test | Man page |

chargaff.gibbs.test | Man page |

chisq.unif.test | Man page |

complement | Man page |

complement.default | Man page |

complement.list | Man page |

complement.SeqFastadna | Man page |

cylinder.counts | Man page |

diffsign.test | Man page |

diid.disturbance | Man page |

diid.test | Man page |

disambiguate | Man page |

disambiguate.default | Man page |

disambiguate.list | Man page |

disambiguate.SeqFastadna | Man page |

estimateMarkovChain | Man page |

ks.unif.test | Man page |

lb.test | Man page |

markov.disturbance | Man page |

markov.test | Man page |

nanoarchaeum | Man page |

oligoCorr | Man page |

oligoProfile | Man page |

pair.counts | Man page |

pieris | Man page |

plot.OligoProfile | Man page |

print.OligoProfile | Man page |

quadruple.counts | Man page |

rank.test | Man page |

rcspr2mat | Man page |

reverseComplement | Man page |

reverseComplement.default | Man page |

reverseComplement.list | Man page |

reverseComplement.SeqFastadna | Man page |

rstochmat | Man page |

rstochvec | Man page |

simulateMarkovChain | Man page |

spgs | Man page |

spgs-package | Man page |

table2vector | Man page |

triple.counts | Man page |

turningpoint.test | Man page |

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

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