MatrixRider-package {MatrixRider} | R Documentation |
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.
Elena Grassi <elena.grassi@unito.it>
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)