scoreNormalization: Normalization of DE/DS scores

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

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, [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

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)

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