scoreNormalization {SeqGSEA} | R Documentation

## Normalization of DE/DS scores

### Description

Normalization of DE/DS scores or permutation DE/DS scores.

### Usage

    scoreNormalization(scores, norm.factor)

### Arguments

`scores` | a vector (a nX1 matrix) of a matrix of scores, rows corresponding to genes and columns corresponding to a study or permutation.
`norm.factor` | normalization factor, output of the function `normFactor`.

### Value

A normalized vector or matrix depending on the input: with the same dimensions as the input.

### Author(s)

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

### References

Xi Wang and Murray J. Cairns (2013). Gene Set Enrichment Analysis of RNA-Seq Data: Integrating Differential Expression and Splicing. BMC Bioinformatics, 14(Suppl 5):S16.

### See Also

`normFactor`

### Examples

    data(RCS_example, package="SeqGSEA")
    permuteMat <- genpermuteMat(RCS_example, times=10)
    RCS_example <- exonTestability(RCS_example)
    RCS_example <- estiExonNBstat(RCS_example)
    RCS_example <- estiGeneNBstat(RCS_example)
    RCS_example <- DSpermute4GSEA(RCS_example, permuteMat)
    ## (not run)
    DSscore.normFac <- normFactor(RCS_example@permute_NBstat_gene)
    DSscore <- scoreNormalization(RCS_example@featureData_gene$NBstat, DSscore.normFac)
    DSscore.perm <- scoreNormalization(RCS_example@permute_NBstat_gene, DSscore.normFac)
    ## End (not run)

[Package SeqGSEA version 1.24.0 Index]