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

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Documentation for package ‘SeqGSEA’ version 1.16.0

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SeqGSEA-package SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data
calES Calculate running enrichment scores of gene sets
calES.perm Calculate enrichment scores for gene sets in the permutation data sets
convertEnsembl2Symbol Convert ensembl gene IDs to gene symbols
convertSymbol2Ensembl Convert gene symbols to ensembl gene IDs
counts Accessors for the 'counts' slot of a ReadCountSet object.
counts-method Accessors for the 'counts' slot of a ReadCountSet object.
counts-methods Accessors for the 'counts' slot of a ReadCountSet object.
counts<--method Accessors for the 'counts' slot of a ReadCountSet object.
DENBStat4GSEA Calculate NB-statistics quantifying differential expression for each gene
DENBStatPermut4GSEA Calculate NB-statistics quantifying DE for each gene in the permutation data sets
DENBTest Perform negative binomial exact test for differential expression
DEpermutePval Permutation for p-values in differential expression analysis
DEscore Pre-calculated DE/DS scores
DEscore.perm Pre-calculated DE/DS scores
DSpermute4GSEA Compute NB-statistics quantifying differential splicing on the permutation data set.
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
DSscore Pre-calculated DE/DS scores
DSscore.perm Pre-calculated DE/DS scores
estiExonNBstat Calculate NB-statistics quantifying differential splicing for individual exons
estiGeneNBstat Calculate NB-statistics quantifying differential splicing for each gene
exonID Accessor to the exonID slot of ReadCountSet objects
exonID<- Accessor to the exonID slot of ReadCountSet objects
exonTestability Check exon testability
geneID Accessor to the geneID slot of ReadCountSet objects
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 object
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 splice scores with a rank-based strategy
RCS_example ReadCountSet object example
ReadCountSet Class '"ReadCountSet"'
ReadCountSet-class Class '"ReadCountSet"'
runDESeq Run DESeq for differential expression analysis
runSeqGSEA An all-in function that allows end users to apply SeqGSEA to their data with one step.
scoreNormalization Normalization of DE/DS scores
SeqGeneSet Class '"SeqGeneSet"'
SeqGeneSet-class Class '"SeqGeneSet"'
SeqGSEA SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data
show-method Class '"SeqGeneSet"'
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
[-method Class '"SeqGeneSet"'