XMatrix-class: '"XMatrix"' objects

In TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

Description

XMatrix is a virtual class. No objects can be created from it directly. Three classes are derived from this class: PFMatrix, PWMatrix and ICMatrix.

PFMatrix is a class whose instances are objects representing raw position frequency matrices (PFMs).

PWMatrix is a class whose instances are objects representing position weight matrices (PWMs). Compared with PFMatrix, it has extra slot pseudocounts.

ICMatrix is a class whose instances are objects representing information content matrices (ICMs). Compared with PWMatrix, it has extra slot schneider.

Usage

## Constructors:
PFMatrix(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())
PWMatrix(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(), pseudocounts=numeric())
ICMatrix(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(), pseudocounts=numeric(),
         schneider=logical())
## Accessor-like methods:
## S4 method for signature 'XMatrix'
ID(x)
## S4 method for signature 'XMatrix'
bg(x)

## ... and more (see Methods)

Arguments

ID	Object of class "character": A unique identifier for each matrix.
name	Object of class "character": The name of the transcription factor. In JASPAR, as far as possible, the name is based on the standardized Entrez gene symbols. In the case the model describes a transcription factor hetero-dimer, two names are concatenated, such as RXR-VDR. In a few cases, different splice forms of the same gene have different binding specificity: in this case the splice form information is added to the name, based on the relevant literature.
matrixClass	Object of class "character": Structural class of the transcription factor, based on the TFCaT system
strand	Object of class "character": Which strand is the binding sites sequences from.
bg	Object of class "numeric": Background frequencies of the four bases. By default, it is equally 0.25.
tags	Object of class "list": Some tags information about this model. Tags include: (1) "family": Structural sub-class of the transcription factor, based on the TFCaT system. (2) "species": The species source for the sequences, in NCBI tax IDs. (3) "tax_group": Group of species, currently consisting of 4 larger groups: vertebrate, insect, plant, chordate. (4) "medline": a ID to the relevant publication reporting the sites used in the mode building. (5) "type": Methodology used for matrix construction. (6) "ACC": A representative protein accession number in Genbank for the transcription factor. Human takes precedence if several exists. (6) "pazar_tf_id": a ID to PAZAR database. (7) "TFBSshape_ID": a ID to TFBSshape database. (8) "TFencyclopedia_ID": a ID to the Transcription Factor Encyclopedia. (9) "comment": For some matrices, a curator comment is added.
profileMatrix	Object of class "matrix": This is the matrix information.
pseudocounts	Object of class "numeric": This is the pseudocounts used when computing ICM or PWM from PFM. By default, a threshold of 0.8 is used based on the previous research (doi:10.1093/nar/gkn1019).
schneider	Obejct of class "logical": this logical value indicates whether the schneider correction is used during the conversion from PFM to ICM.
x	Object of class XMatrix.

Value

A XMatrix object.

Methods

bg

signature(x = "XMatrix"): Gets the background base frequencies.

bg<-

signature(x = "XMatrix"): Sets the background base frequencies.

ID

signature(x = "XMatrix"): Gets the ID information.

ID<-

signature(x = "XMatrix"): Sets the ID information.

length

signature(x = "XMatrix"): Gets the pattern length in nucleotides (i.e. number of columns in the matrix).

reverseComplement

signature(x = "PWMatrix"): Generates the reverse complement matrix object. Note than the strand is XMatrix will also be changed to the opossite strand.

as.matrix

signature(x = "XMatrix"): Returns the matrix in the XMatrix class.

totalIC

signature(x = "ICMatrix"): Returns the information content vector.

Matrix

signature(x = "XMatrix"): Gets the matrix stored in XMatrix object.

Matrix<-

signature(x = "XMatrix"): Sets the matrix stored in XMatrix object.

matrixClass

signature(x = "XMatrix"): Gets the matrix type of a XMatrix object.

matrixClass<-

signature(x = "XMatrix"): Sets the matrix type of a XMatrix object.

name

signature(x = "XMatrix"): Gets the name information.

name<-

signature(x = "XMatrix"): Sets the name information.

strand

signature(x = "XMatrix"): Gets the strand information of a XMatrix object.

tags

signature(x = "XMatrix"): Gets a list object of tags information.

Author(s)

Ge Tan

See Also

toPWM, toICM

Examples

  ## Constructorpf PFMatrix
  ## Note that there is no XMatrix() constructor, 
  ## but an XMatrix family of constructors: PFMatrix(), PWMatrix(), ICMatrix()
  pfm <- PFMatrix(ID="MA0004.1", name="Arnt", matrixClass="Zipper-Type", 
                  strand="+", bg=c(A=0.25, C=0.25, G=0.25, T=0.25), 
                  tags=list(family="Helix-Loop-Helix", species="10090", 
                  tax_group="vertebrates", medline="7592839", type="SELEX", 
                  ACC="P53762", pazar_tf_id="TF0000003",
                  TFBSshape_ID="11", TFencyclopedia_ID="580"),
                  profileMatrix=matrix(c(4,  19, 0,  0,  0,  0,
                                         16, 0,  20, 0,  0,  0,
                                         0,  1,  0,  20, 0,  20,
                                         0,  0,  0,  0,  20, 0), 
                                         byrow=TRUE, nrow=4, 
                                         dimnames=list(c("A", "C", "G", "T")))
                 )
                 
  ## Construction from a set of binding sites sequences
  sitesSeqs <- c("Human Gli1"= "GACCACCCA", "hIGFBP-6"= "GACCCCCCA",
                 "HNF-3beta"="GAACACCCA", "hPlakoglobin"= "GACCACCAA",
                 "rIGFBP-6"= "GTCCACCCA", "Sox-9"= "GGCCACCCA")
  countMatrix <- consensusMatrix(sitesSeqs)
  pfm <- PFMatrix(ID="Gli-1", name="Gli-1", profileMatrix=countMatrix)

  ## Coersion
  as.matrix(pfm)
  as(pfm, "matrix")

  ## Methods
  pwm <- toPWM(pfm)
  reverseComplement(pwm)
  length(pfm)

TFBSTools documentation built on Nov. 8, 2020, 8:14 p.m.