normFactor {SeqGSEA} | R Documentation |
Get normalization factors from permutation scores for normalization DE or DS scores
normFactor(permStat)
permStat |
a matrix of NB-statistics from permutation data sets, with row corresponding to genes and columns to permutations. |
A vector of normalization factors, each for one gene.
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)