spgs: Statistical Patterns in Genomic Sequences
Version 1.0

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("spgs")

Getting started

Package overview

Popular man pages

ag.test: Test of Purine-Pyrimidine Parity Based on Purine Count
chargaff0.test: Vector Test of Chargaff's Second Parity Rule (CSPR) for...
ks.unif.test: Using 'ks.test' to test for Uniformity on the Unit Interval
markov.test: A Test for First-Order Markovianness
nanoarchaeum: DNA sequence for the Nanoarchaeum equitans Kin4-M Chromosome
triple.counts: Count Triplets in Character Vectors
turningpoint.test: The Turning Point Test of Statistical Independence
See all...

All man pages Function index File listing

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

FHatCovariances Source code
FillToSquare Source code
GibbsCovariances Source code
ISPX2mat Source code
ISPX2vec Source code
ag.test Man page Source code
agct.test Man page Source code
agctTestPValue Source code
agctTestPValueFromMonteCarlo Source code
agctTestPValueLowerBound Source code
agctTestPValueLowerBoundTight Source code
agctTestPValueUpperBound Source code
array2vector Man page
charfilter Source code
chargaff.gibbs.test Man page Source code
chargaff0.test Man page Source code
chargaff0testPValue Source code
chargaff0testPValueFromMonteCarlo Source code
chargaff0testPValueLowerBound Source code
chargaff0testPValueLowerBoundTight Source code
chargaff0testPValueUpperBound Source code
chargaff0testPValueUpperBoundTight Source code
chargaff1.test Man page Source code
chargaff1testPValueFromMonteCarlo Source code
chargaff1testPValueFromTable Source code
chargaff1testPValueFromUpperBound Source code
chargaff2.test Man page Source code
chargaff2testPValueFromMonteCarlo Source code
chargaff2testPValueFromMonteCarlo2 Source code
chargaff2testPValueFromTable Source code
chargaff2testPValueFromUpperBound Source code
chisq.unif.test Man page Source code
complement Man page Source code
complement.SeqFastadna Man page Source code
complement.default Man page Source code
complement.list Man page Source code
cyl2lag2.counts Source code
cylinder.counts Man page Source code
diffsign.test Man page Source code
diid.disturbance Man page Source code
diid.test Man page Source code
disambiguate Man page Source code
disambiguate.SeqFastadna Man page Source code
disambiguate.default Man page Source code
disambiguate.list Man page Source code
estimateMarkovChain Man page Source code
ks.unif.test Man page Source code
lb.test Man page Source code
markov.disturbance Man page Source code
markov.test Man page Source code
nanoarchaeum Man page
oligoCorr Man page Source code
oligoProfile Man page Source code
onUnload Source code
pagcttest Source code
pagtestoninterval Source code
pagtestonsimplex Source code
pair.counts Man page Source code
pieris Man page
plot.OligoProfile Man page Source code
print.FiniteStateMarkovChain Source code
print.OligoProfile Man page Source code
print.htest.ext Source code
print.multiplehtests Source code
quadruple.counts Man page Source code
rank.test Man page Source code
rcspr2mat Man page Source code
reverseComplement Man page Source code
reverseComplement.SeqFastadna Man page Source code
reverseComplement.default Man page Source code
reverseComplement.list Man page Source code
rstochmat Man page Source code
rstochvec Man page Source code
simulateMarkovChain Man page Source code
spgs Man page
spgs-package Man page
statdist Source code
strreverse Source code
table2vector Man page
triple.counts Man page Source code
turningpoint.test Man page Source code

Files

configure.ac
tests
tests/profileTest.R
tests/countingTest.R
tests/profileTest.Rout.savefile
tests/countingTest.Rout.savefile
src
src/uint64.h
src/sharedef.h
src/spgs.h
src/spgs.c
src/Makevars.in
src/Makevars.win
NAMESPACE
data
data/nanoarchaeum.rda
data/pieris.rda
data/datalist
R
R/reverseComplement.R
R/chargaff1.test.R
R/complement.R
R/chargaff.gibbs.test.R
R/chargaff2.test.R
R/sysdata.rda
R/profile.R
R/randmat.R
R/MarkovChains.R
R/ag.test.R
R/hooks.R
R/diid.test.R
R/ISPHelpers.R
R/markov.test.R
R/print.R
R/agct.test.R
R/counting.R
R/oligoCorr.R
R/disambiguate.R
R/FHatCovariances.R
R/GibbsCovariances.R
R/chargaff0.test.R
R/auxtests.R
MD5
DESCRIPTION
configure
man
man/oligoProfile.Rd
man/agct.test.Rd
man/rank.test.Rd
man/simulateMarkovChain.Rd
man/rcspr2mat.Rd
man/diffsign.test.Rd
man/triple.counts.Rd
man/turningpoint.test.Rd
man/chargaff1.test.Rd
man/rstochmat.Rd
man/quadruple.counts.Rd
man/diid.test.Rd
man/complement.Rd
man/chargaff0.test.Rd
man/disambiguate.Rd
man/pieris.Rd
man/chisq.unif.test.Rd
man/ag.test.Rd
man/chargaff2.test.Rd
man/ks.unif.test.Rd
man/lb.test.Rd
man/rstochvec.Rd
man/diid.disturbance.Rd
man/nanoarchaeum.Rd
man/markov.test.Rd
man/cylinder.counts.Rd
man/reverseComplement.Rd
man/markov.disturbance.Rd
man/estimateMarkovChain.Rd
man/array2vector.Rd
man/chargaff.gibbs.test.Rd
man/pair.counts.Rd
man/spgs-package.Rd
cleanup
spgs documentation built on May 19, 2017, 7:40 a.m.

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