selex.mmProb: Compute prior probability of sequence using Markov model
In SELEX: Functions for analyzing SELEX-seq data

Description Usage Arguments Value References See Also Examples

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

1	selex.mmProb(seqStr, markovModel)

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

selex.mm returns the prior observation probability of seqStr.

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.

selex.mmProb

# 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)