Calculate total affinity and occupancies for binding site matrices on a given sequence

Description

Calculates a single number for a whole sequence that reflects the propensity of a DNA binding protein to interact with it. The DNA binding protein has to be described with a PFM matrix, for example gotten from Jaspar.

Author(s)

Elena Grassi <elena.grassi@unito.it>

Examples

    library(JASPAR2014)
    library(TFBSTools)
    library(Biostrings)
    pfm <- getMatrixByID(JASPAR2014,"MA0004.1")
## The following sequence has a single perfect match
## thus it gives the same results with all cutoff values.
    sequence <- DNAString("CACGTG")
    getSeqOccupancy(sequence, pfm, 0.1)
    getSeqOccupancy(sequence, pfm, 1)