scoreNormalization {SeqGSEA} | R Documentation |
Normalization of DE/DS scores or permutation DE/DS scores.
scoreNormalization(scores, norm.factor)
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 |
A normalized vector or matrix depending on the input: with the same dimensions as the input.
Xi Wang, xi.wang@newcastle.edu.au
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.
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)