selex.mmProb {SELEX} | R Documentation

## Compute prior probability of sequence using Markov model

### Description

A function used to calculate and return the prior observation probability of a DNA sequence `seqStr` as predicted by Markov model `markovModel`.

### Usage

    selex.mmProb(seqStr, markovModel)

### Arguments

`seqStr` | A character string representing the DNA sequence to be evaluated.
`markovModel` | A Markov model handle.

### Value

`selex.mm` returns the prior observation probability of `seqStr`.

### References

Slattery, M., Riley, T.R., Liu, P., Abe, N., Gomez-Alcala, P., Dror, I., Zhou, T., Rohs, R., Honig, B., Bussemaker, H.J.,and Mann, R.S. (2011) Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 147:1270–1282.

Riley, T.R., Slattery, M., Abe, N., Rastogi, C., Liu, D., Mann, R.S., and Bussemaker, H.J. (2014) SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes. Methods Mol. Biol. 1196:255–278.

### See Also

`selex.mmProb`

### Examples

    # Build the Markov model on the training dataset
    mm = selex.mm(sample=r0.split$train, order=NA, crossValidationSample=r0.split$test)

    # Compute expected Markov model probability value for a random 12-mer
    selex.mmProb(seqStr="ATTGCAGACTTG", markovModel=mm)

[Package SELEX version 1.12.0 Index]