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.
