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.
- Andrew Hart [aut, cre], Servet Martnez [aut], Universidad de Chile [cph], INRIA-Chile [cph]
- Date of publication
- 2015-03-28 07:40:29
- Andrew Hart <email@example.com>
- GPL (>= 2)
- Test of Purine-Pyrimidine Parity Based on Euclidean distance
- Test of Purine-Pyrimidine Parity Based on Purine Count
- Convert Arrays and Tables to Vectors with Named Elements
- Vector Test of Chargaff's Second Parity Rule (CSPR) for...
- Matrix Test of CSPR for Mononucleotides
- Matrix Test of CSPR for Dinucleotides
- Test of CSPR for Dinucleotides Under Gibbs Distribution
- Test of Uniformity Based on Pearsons's Chi-Squared test
- Complement of a DNA/RNA Sequence
- Count Cylinders (Fixed-Offset Patterns) in Character Vectors
- the Differents-Sign Test of Statistical Independence
- Construct feasible Random Noise Generating a Bernoulli...
- A Test for a Bernoulli Scheme (IID Sequence)
- Disambiguate a Nucleic Sequence
- Fit a first-Order Markov Chain to a Sequence of Finite...
- Using 'ks.test' to test for Uniformity on the Unit Interval
- The Ljung-Box Test for Uncorrelated Data
- Construct feasible Random Noise Generating a First-Order...
- A Test for First-Order Markovianness
- DNA sequence for the Nanoarchaeum equitans Kin4-M Chromosome
- Oligo Profiles and Oligo Profile Correlation Plots of...
- Count Pairs in Character Vectors
- DNA sequence for the Pieris Rapae Granulovirus Genome
- Count Quadruplets in Character Vectors
- The Rank Test of Statistical Independence
- Random Stochastic Matrices Complying with Chargaff's Second...
- Reverse Complement of a DNA/RNA Sequence
- Random Generation of Stochastic Matrices
- Random Generation of Stochastic (Probability) Vectors
- Simulate a first-Order Markov Chain
- Statistical Patterns in Genomic Sequences
- Count Triplets in Character Vectors
- The Turning Point Test of Statistical Independence
Files in this package