genpermuteMat: Generate permutation matrix

In sunlightwang/SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

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, [e-mail]

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)

sunlightwang/SeqGSEA documentation built on Dec. 5, 2020, 5:52 p.m.