selex.mmProb {SELEX} | R Documentation |
A function used to calculate and return the prior observation probability of a DNA sequence seqStr
as predicted by Markov model markovModel
.
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.
# 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)