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 Mart<ed>nez
Maintainer: Andrew Hart <ahart@dim.uchile.cl>
Hart, A.G. and Mart<ed>nez, S. (2011) Statistical testing of Chargaff's second parity rule in bacterial genome sequences. Stoch. Models 27(2), 1–46.
Hart, A.G. and Mart<ed>nez, 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 Mart<ed>nez, S. (2012) A Gibbs approach to Chargaff's second parity rule. J. Stat. Phys. 146(2), 408-422. arXiv:1105.0685 [math.pr].
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
Please suggest features or report bugs with the GitHub issue tracker.
All documentation is copyright its authors; we didn't write any of that.
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