XMatrixList-class: Class '"XMatrixList"'

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

Description

The XMatrixList virtual class is a container for storing a collection of XMatrix objects. No object can be constructed directly from this virtual and it has three subclasses: PFMatrixList, PWMatrixList and ICMatrixList. Basically it is a SimpleList and is designed for manipulating the set of XMatrix objects as a whole.

Usage

## Constructors:
PFMatrixList(..., use.names=TRUE)
PWMatrixList(..., use.names=TRUE)
ICMatrixList(..., use.names=TRUE)

## Accessor-like methods:
## S4 method for signature 'XMatrixList'
ID(x)
## S4 method for signature 'XMatrixList'
name(x)
## S4 method for signature 'XMatrixList'
bg(x)
## S4 method for signature 'XMatrixList'
tags(x)
## S4 method for signature 'XMatrixList'
name(x)
## S4 method for signature 'XMatrixList'
strand(x)

Arguments

...	The XMatrix objects are supplied in ....
use.names	A logical value. When TRUE, the names of the XMatrix will be kept.
x	A XMatrixList object.

Value

A XMatrixList object.

Author(s)

Ge Tan

See Also

XMatrix,

Examples

    data(MA0003.2)
    data(MA0004.1)
    
    ## Construction of PFMatrixList
    pfmList <- PFMatrixList(pfm1=MA0003.2, pfm2=MA0004.1, use.names=TRUE)
    
    ## Construction of PFM<atrixList from list of PFMatrix
    pfmList <- do.call(PFMatrixList, list(pfm1=MA0003.2, pfm2=MA0004.1))

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