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spgs (version 1.0-4)

Statistical Patterns in Genomic Sequences

Description

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.

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Version

Install

install.packages('spgs')

Monthly Downloads

286

Version

1.0-4

License

GPL (>= 2)

Maintainer

Andrew Hart

Last Published

October 3rd, 2023

Functions in spgs (1.0-4)

the Differents-Sign Test of Statistical Independence

estimateMarkovChain

Fit a first-Order Markov Chain to a Sequence of Finite Symbols

Nanoarchaeum equitans Kin4-M Chromosome

DNA sequence for the Nanoarchaeum equitans Kin4-M Chromosome

A Test for First-Order Markovianness

diid.disturbance

Construct feasible Random Noise Generating a Bernoulli Process

Disambiguate a Nucleic Sequence

A Test for a Bernoulli Scheme (IID Sequence)

The Ljung-Box Test for Uncorrelated Data

Using ks.test to test for Uniformity on the Unit Interval

simulateMarkovChain

Simulate a first-Order Markov Chain

markov.disturbance

Construct feasible Random Noise Generating a First-Order Markov Chain

Random Generation of Stochastic (Probability) Vectors

Random Stochastic Matrices Complying with Chargaff's Second Parity Rule for Dinucleotides

reverseComplement

Reverse Complement of a DNA/RNA Sequence

The Rank Test of Statistical Independence

Random Generation of Stochastic Matrices

Oligo Profiles and Oligo Profile Correlation Plots of Nucleotide Sequences

Pieris Rapae Granulovirus Genome

DNA sequence for the Pieris Rapae Granulovirus Genome

Count Pairs in Character Vectors

Count Triplets in Character Vectors

tools:::Rd_package_title("spgs")

quadruple.counts

Count Quadruplets in Character Vectors

turningpoint.test

The Turning Point Test of Statistical Independence

Test of Purine-Pyrimidine Parity Based on Euclidean distance

chargaff.gibbs.test

Test of CSPR for Dinucleotides Under Gibbs Distribution

Convert Arrays and Tables to Vectors with Named Elements

chisq.unif.test

Test of Uniformity Based on Pearsons's Chi-Squared test

Complement of a DNA/RNA Sequence

Matrix Test of CSPR for Dinucleotides

cylinder.counts

Count Cylinders (Fixed-Offset Patterns) in Character Vectors

Test of Purine-Pyrimidine Parity Based on Purine Count

Matrix Test of CSPR for Mononucleotides

Vector Test of Chargaff's Second Parity Rule (CSPR) for Mononucleotides