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.
| Version: |
1.0-3 |
| Depends: |
R (≥ 3.0) |
| Imports: |
graphics, stats |
| Enhances: |
seqinr |
| Published: |
2019-12-06 |
| Author: |
Andrew Hart [aut, cre],
Servet MartÃnez [aut],
Universidad de Chile [cph],
INRIA-Chile [cph] |
| Maintainer: |
Andrew Hart <ahart at dim.uchile.cl> |
| License: |
GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Copyright: |
Universidad de Chile, INRIA-Chile |
| NeedsCompilation: |
yes |
| Classification/MSC: |
62F03, 62G10, 62M07, 62P10, 92D20 |
| Citation: |
spgs citation info |
| Materials: |
NEWS |
| CRAN checks: |
spgs results |
Documentation:
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