permuteMatrix-methods: permuteMatrix method

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

Description

This method simply shuffles the columns in matrices. This can either be done by just shuffling columns within each selected matrix, or by shuffling columns almong all selected matrices.

Usage

  permuteMatrix(x, type="intra")

Arguments

x	A matrix which meets the PFM standard, PFMatrix object, or PFMatrixList obejct.
type	The type of shuffling. It can be "intra" or "inter", which shuffle within each matrix, or between all the matrix.

Value

A object with shuffled matrix.

Author(s)

Ge Tan

Examples

    data("MA0043")
    pfmSubject <- MA0043
    data("MA0048")
    pfmQuery <- MA0048
    #opts = list()
    #opts[["class"]] = "Ig-fold"
    #pfmList = getMatrixSet(JASPAR2014, opts)
    pfmList <- PFMatrixList(pfmSubject, pfmQuery)
    foo = permuteMatrix(pfmQuery)
    foo1 = permuteMatrix(pfmList, type="intra")
    foo2 = permuteMatrix(pfmList, type="inter")

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