MatrixRider-package: Calculate total affinity and occupancies for binding site...
In MatrixRider: Obtain total affinity and occupancies for binding site matrices on a given sequence
Description
Author(s)
Examples
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
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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)
MatrixRider documentation built on Nov. 8, 2020, 8:25 p.m.
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Description Author(s) Examples
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
1 2 3 4 5 6 7 8 9 | 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)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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