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

spgs (version 1.0-1)

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

276

Version

1.0-1

License

GPL (>= 2)

Maintainer

Andrew Hart

Last Published

July 21st, 2017

Functions in spgs (1.0-1)

chargaff0.test

Vector Test of Chargaff's Second Parity Rule (CSPR) for Mononucleotides
chargaff1.test

Matrix Test of CSPR for Mononucleotides
array2vector

Convert Arrays and Tables to Vectors with Named Elements
chargaff.gibbs.test

Test of CSPR for Dinucleotides Under Gibbs Distribution
diffsign.test

the Differents-Sign Test of Statistical Independence
diid.disturbance

Construct feasible Random Noise Generating a Bernoulli Process
oligoProfile

Oligo Profiles and Oligo Profile Correlation Plots of Nucleotide Sequences
pair.counts

Count Pairs in Character Vectors
chargaff2.test

Matrix Test of CSPR for Dinucleotides
chisq.unif.test

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

Fit a first-Order Markov Chain to a Sequence of Finite Symbols
ks.unif.test

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

Reverse Complement of a DNA/RNA Sequence
rstochmat

Random Generation of Stochastic Matrices
ag.test

Test of Purine-Pyrimidine Parity Based on Purine Count
agct.test

Test of Purine-Pyrimidine Parity Based on Euclidean distance
diid.test

A Test for a Bernoulli Scheme (IID Sequence)
disambiguate

Disambiguate a Nucleic Sequence
rstochvec

Random Generation of Stochastic (Probability) Vectors
lb.test

The Ljung-Box Test for Uncorrelated Data
markov.disturbance

Construct feasible Random Noise Generating a First-Order Markov Chain
Pieris Rapae Granulovirus Genome

DNA sequence for the Pieris Rapae Granulovirus Genome
quadruple.counts

Count Quadruplets in Character Vectors
simulateMarkovChain

Simulate a first-Order Markov Chain
spgs-package

Statistical Patterns in Genomic Sequences
triple.counts

Count Triplets in Character Vectors
complement

Complement of a DNA/RNA Sequence
cylinder.counts

Count Cylinders (Fixed-Offset Patterns) in Character Vectors
markov.test

A Test for First-Order Markovianness
Nanoarchaeum equitans Kin4-M Chromosome

DNA sequence for the Nanoarchaeum equitans Kin4-M Chromosome
rank.test

The Rank Test of Statistical Independence
rcspr2mat

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

The Turning Point Test of Statistical Independence