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.
|Author||Andrew Hart [aut, cre], Servet Martnez [aut], Universidad de Chile [cph], INRIA-Chile [cph]|
|Date of publication||2015-03-28 07:40:29|
|Maintainer||Andrew Hart <firstname.lastname@example.org>|
|License||GPL (>= 2)|
agct.test: Test of Purine-Pyrimidine Parity Based on Euclidean distance
ag.test: Test of Purine-Pyrimidine Parity Based on Purine Count
array2vector: Convert Arrays and Tables to Vectors with Named Elements
chargaff0.test: Vector Test of Chargaff's Second Parity Rule (CSPR) for...
chargaff1.test: Matrix Test of CSPR for Mononucleotides
chargaff2.test: Matrix Test of CSPR for Dinucleotides
chargaff.gibbs.test: Test of CSPR for Dinucleotides Under Gibbs Distribution
chisq.unif.test: Test of Uniformity Based on Pearsons's Chi-Squared test
complement: 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...
diid.test: A Test for a Bernoulli Scheme (IID Sequence)
disambiguate: Disambiguate a Nucleic Sequence
estimateMarkovChain: Fit a first-Order Markov Chain to a Sequence of Finite...
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.test: A Test for First-Order Markovianness
nanoarchaeum: DNA sequence for the Nanoarchaeum equitans Kin4-M Chromosome
oligoProfile: Oligo Profiles and Oligo Profile Correlation Plots of...
pair.counts: Count Pairs in Character Vectors
pieris: DNA sequence for the Pieris Rapae Granulovirus Genome
quadruple.counts: Count Quadruplets in Character Vectors
rank.test: The Rank Test of Statistical Independence
rcspr2mat: Random Stochastic Matrices Complying with Chargaff's Second...
reverseComplement: 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-package: Statistical Patterns in Genomic Sequences
triple.counts: Count Triplets in Character Vectors
turningpoint.test: The Turning Point Test of Statistical Independence