spgs: Statistical Patterns in Genomic Sequences

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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

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