Man pages for SeqGSEA
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
| calES | Calculate running enrichment scores of gene sets |
| calES.perm | Calculate enrichment scores for gene sets in the permutation... |
| convertEnsembl2Symbol | Convert ensembl gene IDs to gene symbols |
| convertSymbol2Ensembl | Convert gene symbols to ensembl gene IDs |
| counts-methods | Accessors for the 'counts' slot of a ReadCountSet object. |
| DENBStat4GSEA | Calculate NB-statistics quantifying differential expression... |
| DENBStatPermut4GSEA | Calculate NB-statistics quantifying DE for each gene in the... |
| DENBTest | Perform negative binomial exact test for differential... |
| DEpermutePval | Permutation for p-values in differential expression analysis |
| DEscore | Pre-calculated DE/DS scores |
| DSpermute4GSEA | Compute NB-statistics quantifying differential splicing on... |
| DSpermutePval | Permutation for p-values in differential splicing analysis |
| DSresultExonTable | Form a table for DS analysis results at the Exon level |
| DSresultGeneTable | Form a table for DS analysis results at the gene level |
| estiExonNBstat | Calculate NB-statistics quantifying differential splicing for... |
| estiGeneNBstat | Calculate NB-statistics quantifying differential splicing for... |
| exonID | Accessor to the exonID slot of ReadCountSet objects |
| exonTestability | Check exon testability |
| geneID | Accessor to the geneID slot of ReadCountSet objects |
| geneList | Get the gene list in a SeqGeneSet object |
| genePermuteScore | Calculate gene scores on permutation data sets |
| geneScore | Calculate gene scores by integrating DE and DS scores |
| geneSetDescs | Get the descriptions of gene sets in a SeqGeneSet object |
| geneSetNames | Get the names of gene set in a SeqGeneSet object |
| geneSetSize | Get the numbers of genes in each gene set in a SeqGeneSet... |
| geneTestability | Check gene testability |
| genpermuteMat | Generate permutation matrix |
| getGeneCount | Calculate read counts of genes from a ReadCountSet object |
| GSEAresultTable | Form a table for GSEA results |
| GSEnrichAnalyze | Main function of gene set enrichment analysis |
| GS_example | SeqGeneSet object example |
| label | Get the labels of samples in a ReadCountSet object |
| loadExonCountData | Load Exon Count Data |
| loadGenesets | Load gene sets from files |
| newGeneSets | Initialize a new SeqGeneSet object |
| newReadCountSet | Generate a new ReadCountSet object |
| normES | Normalize enrichment scores |
| normFactor | Get normalization factors for normalization DE or DS scores |
| plotES | Plot the distribution of enrichment scores |
| plotGeneScore | Plot gene (DE/DS) scores |
| plotSig | Plot showing SeqGeneSet's p-values/FDRs vs. NESs |
| plotSigGeneSet | Plot gene set details |
| rankCombine | Integration of differential expression and differential... |
| RCS_example | ReadCountSet object example |
| ReadCountSet-class | Class '"ReadCountSet"' |
| runDESeq | Run DESeq for differential expression analysis |
| runSeqGSEA | An all-in function that allows end users to apply SeqGSEA to... |
| scoreNormalization | Normalization of DE/DS scores |
| SeqGeneSet-class | Class '"SeqGeneSet"' |
| SeqGSEA-package | SeqGSEA: a Bioconductor package for gene set enrichment... |
| signifES | Calculate significance of ESs |
| size | Number of gene sets in a SeqGeneSet object |
| subsetByGenes | Get a new ReadCountSet with specified gene IDs. |
| topDEGenes | Extract top differentially expressed genes. |
| topDSExons | Extract top differentially spliced exons |
| topDSGenes | Extract top differentially spliced genes |
| topGeneSets | Extract top significant gene sets |
| writeScores | Write DE/DS scores and gene scores |
| writeSigGeneSet | Write gene set supporting information |
