normFactor {SeqGSEA} | R Documentation

## Get normalization factors for normalization DE or DS scores

### Description

Get normalization factors from permutation scores for normalization DE or DS scores

### Usage

    normFactor(permStat)

### Arguments

`permStat` | a matrix of NB-statistics from permutation data sets, with row corresponding to genes and columns to permutations.

### Value

A vector of normalization factors, each for one gene.

### 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

`scoreNormalization`

### 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 1.27.0 Index]