Package: spgs 1.0-4

Andrew Hart

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.

Authors:Andrew Hart [aut, cre], Servet Martínez [aut], Universidad de Chile [cph], INRIA-Chile [cph]

spgs_1.0-4.tar.gz
spgs_1.0-4.tar.gz(r-4.5-noble)spgs_1.0-4.tar.gz(r-4.4-noble)
spgs_1.0-4.tgz(r-4.4-emscripten)spgs_1.0-4.tgz(r-4.3-emscripten)
spgs.pdf |spgs.html✨
spgs/json (API)
NEWS

# Install 'spgs' in R:
install.packages('spgs', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • nanoarchaeum - DNA sequence for the Nanoarchaeum equitans Kin4-M Chromosome
  • pieris - DNA sequence for the Pieris Rapae Granulovirus Genome

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.97 score 93 scripts 412 downloads 32 exports 0 dependencies

Last updated 1 years agofrom:987257510f. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-linux-x86_64NOTENov 18 2024

Exports:ag.testagct.testarray2vectorchargaff.gibbs.testchargaff0.testchargaff1.testchargaff2.testchisq.unif.testcomplementcylinder.countsdiffsign.testdiid.disturbancediid.testdisambiguateestimateMarkovChainks.unif.testlb.testmarkov.disturbancemarkov.testoligoCorroligoProfilepair.countsquadruple.countsrank.testrcspr2matreverseComplementrstochmatrstochvecsimulateMarkovChaintable2vectortriple.countsturningpoint.test

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Statistical Patterns in Genomic Sequencesspgs-package spgs
Test of Purine-Pyrimidine Parity Based on Purine Countag.test
Test of Purine-Pyrimidine Parity Based on Euclidean distanceagct.test
Convert Arrays and Tables to Vectors with Named Elementsarray2vector table2vector
Test of CSPR for Dinucleotides Under Gibbs Distributionchargaff.gibbs.test
Vector Test of Chargaff's Second Parity Rule (CSPR) for Mononucleotideschargaff0.test
Matrix Test of CSPR for Mononucleotideschargaff1.test
Matrix Test of CSPR for Dinucleotideschargaff2.test
Test of Uniformity Based on Pearsons's Chi-Squared testchisq.unif.test
Complement of a DNA/RNA Sequencecomplement complement.default complement.list complement.SeqFastadna
Count Cylinders (Fixed-Offset Patterns) in Character Vectorscylinder.counts
the Differents-Sign Test of Statistical Independencediffsign.test
Construct feasible Random Noise Generating a Bernoulli Processdiid.disturbance
A Test for a Bernoulli Scheme (IID Sequence)diid.test
Disambiguate a Nucleic Sequencedisambiguate disambiguate.default disambiguate.list disambiguate.SeqFastadna
Fit a first-Order Markov Chain to a Sequence of Finite SymbolsestimateMarkovChain
Using 'ks.test' to test for Uniformity on the Unit Intervalks.unif.test
The Ljung-Box Test for Uncorrelated Datalb.test
Construct feasible Random Noise Generating a First-Order Markov Chainmarkov.disturbance
A Test for First-Order Markoviannessmarkov.test
DNA sequence for the Nanoarchaeum equitans Kin4-M Chromosomenanoarchaeum
Oligo Profiles and Oligo Profile Correlation Plots of Nucleotide SequencesoligoCorr oligoProfile plot.OligoProfile print.OligoProfile
Count Pairs in Character Vectorspair.counts
DNA sequence for the Pieris Rapae Granulovirus Genomepieris
Count Quadruplets in Character Vectorsquadruple.counts
The Rank Test of Statistical Independencerank.test
Random Stochastic Matrices Complying with Chargaff's Second Parity Rule for Dinucleotidesrcspr2mat
Reverse Complement of a DNA/RNA SequencereverseComplement reverseComplement.default reverseComplement.list reverseComplement.SeqFastadna
Random Generation of Stochastic Matricesrstochmat
Random Generation of Stochastic (Probability) Vectorsrstochvec
Simulate a first-Order Markov ChainsimulateMarkovChain
Count Triplets in Character Vectorstriple.counts
The Turning Point Test of Statistical Independenceturningpoint.test