spgs-package | R Documentation |
provides functions for exploring and testing statistical properties and patterns in DNA sequences.
Package: | spgs |
Type: | Package |
License: | GPL (>= 2) |
This package provides a range of statistical tests for various properties of DNA and/or other genomic sequences. There are eight groups of functions:
chargaff0.test
, chargaff1.test
, chargaff2.test
,
chargaff.gibbs.test
, oligoProfile
ag.test
, agct.test
markov.test
, diid.test
diffsign.test
, turningpoint.test
,
rank.test
, lb.test
ks.unif.test
, chisq.unif.test
simulateMarkovChain
, estimateMarkovChain
,
rstochvec
, rstochmat
, rcspr2mat
complement
, reverseComplement
pair.counts
, triple.counts
, quadruple.counts
, cylinder.counts
The word/k-mer counting functions are general and can deal with arbitrary symbolic sequences, not only DNA sequences.
Functions which take a DNA sequence as input are able to work with sequences
stored as SeqFastadna
objects generated by the seqinr package.
Andrew Hart and Servet Martínez
Maintainer: Andrew Hart <ahart@dim.uchile.cl>
Hart, A.G. and Martínez, S. (2011) Statistical testing of Chargaff's second parity rule in bacterial genome sequences. Stoch. Models 27(2), 1–46.
Hart, A.G. and Martínez, S. (2014) Markovianness and Conditional Independence in Annotated Bacterial DNA. Stat. Appl. Genet. Mol. Biol. 13(6), 693-716. arXiv:1311.4411 [q-bio.QM].
Hart, A.G. and Martínez, S. (2012) A Gibbs approach to Chargaff's second parity rule. J. Stat. Phys. 146(2), 408-422. arXiv:1105.0685 [math.pr].
seqinr
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