TFBSTools (version 1.10.3)

permuteMatrix-methods: permuteMatrix method

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.

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")