normFactor: Get normalization factors for normalization DE or DS scores

Description Usage Arguments Value Author(s) References See Also Examples

Description

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

Usage

1
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

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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)


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