permuteMatrix-methods {TFBSTools} | R Documentation

## 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.

### 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")

[Package TFBSTools version 1.28.0 Index]