Learn R Programming

⚠️There's a newer version (1.0-4) of this package.Take me there.

spgs (version 1.0-3)

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.

Copy Link

Version

Install

install.packages('spgs')

Monthly Downloads

317

Version

1.0-3

License

GPL (>= 2)

Maintainer

Andrew Hart

Last Published

December 6th, 2019

Functions in spgs (1.0-3)

the Differents-Sign Test of Statistical Independence

Complement of a DNA/RNA Sequence

Count Pairs in Character Vectors

Oligo Profiles and Oligo Profile Correlation Plots of Nucleotide Sequences

diid.disturbance

Construct feasible Random Noise Generating a Bernoulli Process

turningpoint.test

The Turning Point Test of Statistical Independence

Convert Arrays and Tables to Vectors with Named Elements

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

chargaff.gibbs.test

Test of CSPR for Dinucleotides Under Gibbs Distribution

markov.disturbance

Construct feasible Random Noise Generating a First-Order Markov Chain

cylinder.counts

Count Cylinders (Fixed-Offset Patterns) in Character Vectors

estimateMarkovChain

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

reverseComplement

Reverse Complement of a DNA/RNA Sequence

A Test for First-Order Markovianness

Pieris Rapae Granulovirus Genome

DNA sequence for the Pieris Rapae Granulovirus Genome

quadruple.counts

Count Quadruplets in Character Vectors

Count Triplets in Character Vectors

Nanoarchaeum equitans Kin4-M Chromosome

DNA sequence for the Nanoarchaeum equitans Kin4-M Chromosome

The Ljung-Box Test for Uncorrelated Data

Random Generation of Stochastic (Probability) Vectors

simulateMarkovChain

Simulate a first-Order Markov Chain

Random Generation of Stochastic Matrices

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

The Rank Test of Statistical Independence

Matrix Test of CSPR for Mononucleotides

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

Test of Purine-Pyrimidine Parity Based on Euclidean distance

Test of Purine-Pyrimidine Parity Based on Purine Count

Matrix Test of CSPR for Dinucleotides

Disambiguate a Nucleic Sequence

A Test for a Bernoulli Scheme (IID Sequence)

chisq.unif.test

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