Generate permutation matrix

Description

Generate permutation matrix from ReadCountSet objects or from label vectors.

Usage

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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

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

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