Gene Set Uncertainty in Enrichment Analysis


[Up] [Top]

Documentation for package ‘GiANT’ version 1.3.4

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