# Gene Set Uncertainty in Enrichment Analysis

## Documentation for package ‘GiANT’ version 1.3.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

analysis.averageCorrelation | Predefined enrichment analyses
analysis.averageTStatistic | Predefined enrichment analyses
analysis.customOverrepresentation | Predefined enrichment analyses
analysis.globalAncova | Predefined enrichment analyses
analysis.globalTest | Predefined enrichment analyses
analysis.gsea | Predefined enrichment analyses
analysis.overrepresentation | Predefined enrichment analyses
countdata | Example data
createSummaryTable | Create an overview table for an analysis
evaluateGeneSetUncertainty | Quantify gene set uncertainty
filterGeneSets | Filtering of gene sets
geneSetAnalysis | Main interface for enrichment analyses.
GiANT | Enrichment analysis
global | Global analyses
global.ancova | Global analyses
global.overrepresentation | Global analyses
global.test | Global analyses
gls | Gene-level statistics
gls.cor | Gene-level statistics
gls.foldChange | Gene-level statistics
gls.moderateTStatistic | Gene-level statistics
gls.nBinomTest | Gene-level statistics
gls.regression | Gene-level statistics
gls.tStatistic | Gene-level statistics
gsAnalysis | Gene set analysis.
gss | Gene set statistics
gss.enrichmentScore | Gene set statistics
gss.fisherExactTest | Gene set statistics
gss.gsz | Gene set statistics
gss.maxmean | Gene set statistics
gss.mean | Gene set statistics
gss.median | Gene set statistics
gss.sum | Gene set statistics
gss.wilcoxonRankTest | Gene set statistics
hist.gsaResult | Null distribution histogram and statistic of the input set for enrichment analyses.
labels | Example data to label samples in countdata (rows) in two classes 0 and 1
mergeProbesForGenes | Merge multiple probes for one gene
parseGmt | Venn Euler Diagramm
pathways | Example data for pathways to to gene set enrichtment analyses
plot.uncertaintyResult | Plots the results of an uncertainty analysis.
plotOverrepresentation | Plot overlap of gene sets and core set
predefinedAnalyses | Predefined enrichment analyses
preprocessGeneSets | Eliminate unknown genes from gene sets
preprocessGs | Eliminate unknown genes from gene sets
significance | Significance assessment
significance.permutation | Significance assessment
significance.restandardization | Significance assessment
significance.sampling | Significance assessment
summary.gsaResult | Summarize gene set analysis results
transformation | Transformations
transformation.abs | Transformations
transformation.adjust | Transformations
transformation.adjustAndBinarize | Transformations
transformation.binarize | Transformations
transformation.localFdr | Transformations
transformation.rank | Transformations
transformation.square | Transformations