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

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.