# Build Markov Model to represent sequences in an MS object

### Description

Build a Markov Model of user specified order to represent sequences in an MS object.

### Usage

1 |

### Arguments

`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 |

### Value

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).

### See Also

`read.ms split.ms groupByGC.ms`

### Examples

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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