genpermuteMat {SeqGSEA} | R Documentation |
Generate permutation matrix from ReadCountSet objects or from label vectors.
genpermuteMat(obj, times = 1000, seed = NULL)
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. |
A sample label shuffled matrix, rows corresponding to samples and columns for each permutation.
Xi Wang, xi.wang@newcastle.edu.au
DSpermute4GSEA
,
DENBStatPermut4GSEA
data(RCS_example, package="SeqGSEA") permuteMat <- genpermuteMat(RCS_example, times=10, seed=0) RCS_example <- exonTestability(RCS_example) RCS_example <- DSpermute4GSEA(RCS_example, permuteMat)