TFFM {TFBSTools} | R Documentation |
The TFFM is a virtual class. Two classes are derived from this class: TFFMFirst and TFFMDetail.
TFFMFirst class stands for the first-order TFFMs and TFFMDetail stands for the more detailed and descriptive TFFMs.
## constructors: TFFMFirst(ID="Unknown", name="Unknown", matrixClass="Unknown", strand="+", bg=c(A=0.25, C=0.25, G=0.25, T=0.25), tags=list(), profileMatrix=matrix(), type=character(), emission=list(), transition=matrix()) TFFMDetail(ID="Unknown", name="Unknown", matrixClass="Unknown", strand="+", bg=c(A=0.25, C=0.25, G=0.25, T=0.25), tags=list(), profileMatrix=matrix(), type=character(), emission=list(), transition=matrix())
ID,name,matrixClass,strand,bg,tags,profileMatrix |
See |
type |
The type of TFFM. |
emission |
The emission distribution parameters. |
transition |
The transition probability matrix. |
A TFFM
object.
signature(x = "TFFMFirst")
:
Get the length of First-order TFFM.
signature(x = "TFFMDetail")
:
Get the length of detail TFFM.
signature(x = "TFFM")
:
Get the information content at each position.
Ge Tan
Mathelier, A., and Wasserman, W.W. (2013). The next generation of transcription factor binding site prediction. PLoS Comput. Biol. 9, e1003214.
http://cisreg.cmmt.ubc.ca/TFFM/doc/#
xmlFirst <- file.path(system.file("extdata", package="TFBSTools"), "tffm_first_order.xml") tffmFirst <- readXMLTFFM(xmlFirst, type="First") tffm <- getPosProb(tffmFirst)