normFactor: Get normalization factors for normalization DE or DS scores

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

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, [e-mail]

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)

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