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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.
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Package details |
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| Author | Andrew Hart [aut, cre], Servet MartÃnez [aut], Universidad de Chile [cph], INRIA-Chile [cph] |
| Maintainer | Andrew Hart <ahart@dim.uchile.cl> |
| License | GPL (>= 2) |
| Version | 1.0-4 |
| Package repository | View on CRAN |
| Installation |
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