genpermuteMat {SeqGSEA} | R Documentation

## Generate permutation matrix

### Description

Generate permutation matrix from ReadCountSet objects or from label vectors.

### Usage

    genpermuteMat(obj, times = 1000, seed = NULL)

### Arguments

`obj` | a ReadCountSet object or a label vector. This function needs the original sample label information to generate permutation matrix.
`times` | an integer indication the times of permutation.
`seed` | an integer or NULL, to produce the random seed (an integer vector) for generating random permutation matrix: the same seed generates the same permutation matrix, which is introduced for reproducibility.

### Value

A sample label shuffled matrix, rows corresponding to samples and columns for each permutation.

### Author(s)

Xi Wang, xi.wang@newcastle.edu.au

### See Also

`DSpermute4GSEA`, `DENBStatPermut4GSEA`

### Examples

    data(RCS_example, package="SeqGSEA")
    permuteMat <- genpermuteMat(RCS_example, times=10, seed=0)
    RCS_example <- exonTestability(RCS_example)
    RCS_example <- DSpermute4GSEA(RCS_example, permuteMat)

[Package SeqGSEA version 1.34.0 Index]