Build a Markov Model of user specified order to represent sequences in an MS object.
1 
ms 
Sequence used to build Markov Model 
order 
Order of Markov model to build; ie, the number of preceding bases to consider when calculating the probability of a given base. 
pseudoCount 
(Optional) Integer added to the number of observed cases of each possible sequence pattern. 
considerReverse 
(Optional) Logical value. If 
A list of matrices, each representing a markov model from order 0, 1, ..., order. Each matrix gives the probability of observing a particular base (column) given the preceding bases (row).
read.ms split.ms groupByGC.ms
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15  require("rtfbs")
exampleArchive < system.file("extdata", "NRSF.zip", package="rtfbs")
seqFile < "input.fas"
unzip(exampleArchive, seqFile)
# Read in FASTA file "input.fas" from the examples into an
# MS (multiple sequences) object
ms < read.ms(seqFile)
# Build a 3rd order Markov Model to represent the sequences
# in the MS object "ms". The Model will be a list of
# matrices corrisponding in size to the order of the
# Markov Model
mm < build.mm(ms, 3);
# Print the list of 4 Markov Matrices that make up the
# Markov Model
print(mm)

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