markovModel: Markov model for generating Y_1Y_2_Y3 ...
In motifcounter: R package for analysing TFBSs in DNA sequences

Description Usage Arguments Details Value See Also Examples

This function implements the Markov model for producing motif matches. The function takes a state probability vector and uses the transition probabilities in order to obtain the state probability at the next time point. This function is used used to determine the stationary distribution of the states.

1	markovModel(overlap, nsteps = 1)

`overlap`	An Overlap object.
`nsteps`	Number of state transitions to perform

The R interface is only used for the purpose of testing the correctness of the model.

List containing

dist: State probability distribution after the given number of steps

compoundPoissonDist

numMotifHits

probOverlapHit

# Load sequences
seqfile = system.file("extdata", "seq.fasta", package = "motifcounter")
seqs = Biostrings::readDNAStringSet(seqfile)

# Load motif
motiffile = system.file("extdata", "x31.tab", package = "motifcounter")
motif = t(as.matrix(read.table(motiffile)))

# Load background model
bg = readBackground(seqs, 1)

# Compute overlap probabilities
op = motifcounter:::probOverlapHit(motif, bg, singlestranded = FALSE)


# Computes the state probabilities of the Markov model
# (default: after one step)
dist = motifcounter:::markovModel(op)