R: Statistical Patterns in Genomic Sequences

# Statistical Patterns in Genomic Sequences

## Documentation for package ‘spgs’ version 1.0-4

- DESCRIPTION file
- Package NEWS

## Help Pages

spgs-package | Statistical Patterns in Genomic Sequences
ag.test | Test of Purine-Pyrimidine Parity Based on Purine Count
agct.test | Test of Purine-Pyrimidine Parity Based on Euclidean distance
array2vector | Convert Arrays and Tables to Vectors with Named Elements
chargaff.gibbs.test | Test of CSPR for Dinucleotides Under Gibbs Distribution
chargaff0.test | Vector Test of Chargaff's Second Parity Rule (CSPR) for Mononucleotides
chargaff1.test | Matrix Test of CSPR for Mononucleotides
chargaff2.test | Matrix Test of CSPR for Dinucleotides
chisq.unif.test | Test of Uniformity Based on Pearsons's Chi-Squared test
complement | Complement of a DNA/RNA Sequence
complement.default | Complement of a DNA/RNA Sequence
complement.list | Complement of a DNA/RNA Sequence
complement.SeqFastadna | 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 Process
diid.test | A Test for a Bernoulli Scheme (IID Sequence)
disambiguate | Disambiguate a Nucleic Sequence
disambiguate.default | Disambiguate a Nucleic Sequence
disambiguate.list | Disambiguate a Nucleic Sequence
disambiguate.SeqFastadna | Disambiguate a Nucleic Sequence
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
lb.test | The Ljung-Box Test for Uncorrelated Data
markov.disturbance | Construct feasible Random Noise Generating a First-Order Markov Chain
markov.test | A Test for First-Order Markovianness
nanoarchaeum | DNA sequence for the Nanoarchaeum equitans Kin4-M Chromosome
oligoCorr | Oligo Profiles and Oligo Profile Correlation Plots of Nucleotide Sequences
oligoProfile | Oligo Profiles and Oligo Profile Correlation Plots of Nucleotide Sequences
pair.counts | Count Pairs in Character Vectors
pieris | DNA sequence for the Pieris Rapae Granulovirus Genome
plot.OligoProfile | Oligo Profiles and Oligo Profile Correlation Plots of Nucleotide Sequences
print.OligoProfile | Oligo Profiles and Oligo Profile Correlation Plots of Nucleotide Sequences
quadruple.counts | Count Quadruplets in Character Vectors
rank.test | The Rank Test of Statistical Independence
rcspr2mat | Random Stochastic Matrices Complying with Chargaff's Second Parity Rule for Dinucleotides
reverseComplement | Reverse Complement of a DNA/RNA Sequence
reverseComplement.default | Reverse Complement of a DNA/RNA Sequence
reverseComplement.list | Reverse Complement of a DNA/RNA Sequence
reverseComplement.SeqFastadna | 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 | Statistical Patterns in Genomic Sequences
table2vector | Convert Arrays and Tables to Vectors with Named Elements
triple.counts | Count Triplets in Character Vectors
turningpoint.test | The Turning Point Test of Statistical Independence