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.

AuthorAndrew Hart [aut, cre], Servet Martnez [aut], Universidad de Chile [cph], INRIA-Chile [cph]
Date of publication2015-03-28 07:40:29
MaintainerAndrew Hart <ahart@dim.uchile.cl>
LicenseGPL (>= 2)
Version1.0

View on CRAN

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

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