computeClumpStartProb: Computes the Clump start probability based on a Markov model
In motifcounter: R package for analysing TFBSs in DNA sequences

Description Usage Arguments Details Value See Also Examples

This function leverages a Markov model in order to determine the clump start probability. The computation depends on the selected false positive probability for calling motif matches 'alpha' and the pre-determined overlapping match probabilities 'beta'.

1	computeClumpStartProb(overlap)

overlap

An Overlap object.

The general idea of the method relies on the fact that for the stationary distribution of the Markov model, motif matches must be observed with probability 'alpha'. Hence, the clump start probability 'tau' is optimized to achieve that goal.

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

Clump start probability 'tau'

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 clump start probability
dist = motifcounter:::computeClumpStartProb(op)