Function reference • myTAI

All functions
`CollapseReplicates()`	Combine Replicates in an ExpressionSet
`CombinatorialSignificance()`	Compute the Statistical Significance of Each Replicate Combination
`DiffGenes()`	Differential Gene Expression Analysis
`DivergenceExpressionSetExample`	An Example DivergenceExpressionSet Data Set
`EarlyConservationTest()`	Perform Reductive Early Conservation Test
`EnrichmentTest()`	Phylostratum or Divergence Stratum Enrichment of a given Gene Set based on Fisher's Test
`Expressed()`	Filter for Expressed Genes
`FlatLineTest()`	Perform Flat Line Test
`GroupDiffs()`	Quantify the significant differences between gene expression distributions of age groups
`LateConservationTest()`	Perform Reductive Late Conservation Test
`MatchMap()`	Match a Phylostratigraphic Map or Divergence Map with a ExpressionMatrix
`PhyloExpressionSetExample`	An Example PhyloExpressionSet Data Set
`PlotBarRE()`	Plot Mean Relative Expression Levels as Barplot
`PlotCIRatio()`	Plot Transcriptome Index using bootstrapping and confidence intervals
`PlotCategoryExpr()`	Plot the Expression Levels of each Age or Divergence Category as Boxplot, Violinplot, or Dotplot
`PlotContribution()`	Plot Cumulative Transcriptome Index
`PlotCorrelation()`	Plot the Correlation Between Phylostrata and Divergence Strata
`PlotDistribution()`	Plot the Frequency Distribution of Phylostrata or Divergence Strata
`PlotEnrichment()`	Plot the Phylostratum or Divergence Stratum Enrichment of a given Gene Set
`PlotGeneSet()`	Plot the Expression Profiles of a Gene Set
`PlotGroupDiffs()`	Plot the significant differences between gene expression distributions of PS or DS groups
`PlotMeans()`	Plot Mean Expression Profiles
`PlotMedians()`	Plot Median Expression Profiles
`PlotPattern()`	Plot the Transcriptome Age Index or Transcriptome Divergence Index
`PlotRE()`	Plot Relative Expression Levels
`PlotReplicateQuality()`	Plot the Quality of Biological Replicates
`PlotSelectedAgeDistr()`	Plot the PS or DS distribution of a selected set of genes
`PlotSignature()`	Plot evolutionary signatures across transcriptomes
`PlotSignatureTransformed()`	Plot evolutionary signatures across transcriptomes and RNA-seq transformations
`PlotVars()`	Plot Variance of Expression Profiles
`RE()`	Transform to Relative Expression Levels
`REMatrix()`	Compute a Relative Expression Matrix
`ReductiveHourglassTest()`	Perform the Reductive Hourglass Test
`ReverseHourglassTest()`	Perform the Reverse Hourglass Test
`SelectGeneSet()`	Select a Subset of Genes in an ExpressionSet
`TAI()`	Compute the Transcriptome Age Index (TAI)
`TDI()`	Compute the Transcriptome Divergence Index (TDI)
`TEI()`	Compute the Transcriptome Evolutionary Index (TEI)
`TPI()`	Compute the Transcriptome Polymorphism Index (TPI)
`age.apply()`	Age Category Specific apply Function
`bar.colors()`	Color palette for barplots
`bootMatrix()`	Compute a Permutation Matrix for Test Statistics
`bootTEI()`	Compute a Permutation Matrix of Transcriptome Evolutionary Index (TEI)
`ecScore()`	Compute the Hourglass Score for the EarlyConservationTest
`geom.mean()`	Geometric Mean
`harm.mean()`	Harmonic Mean
`is.ExpressionSet()`	Test ExpressionSet Standard
`lcScore()`	Compute the Hourglass Score for the LateConservationTest
`omitMatrix()`	Compute TAI or TDI Profiles Omitting a Given Gene
`pMatrix()`	Compute Partial TAI or TDI Values
`pMatrixTEI()`	Compute Partial Transcriptome Evolutionary Index (TEI) Values
`pStrata()`	Compute Partial Strata Values
`pStrataTEI()`	Compute Partial Transcriptome Evolutionary Index (TEI) Strata Values
`pTAI()`	Compute the Phylostratum Contribution to the Global Transcriptome Age Index
`pTDI()`	Compute the Divergence Stratum Contribution to the Global Transcriptome Divergence Index
`rcpp_boottei_parallel()`	rcpp_boottei_parallel
`rcpp_pMatrix_parallel()`	rcpp_pMatrix_parallel
`rcpp_pStrata_parallel()`	rcpp_pStrata_parallel
`rcpp_tei_parallel()`	rcpp_tei_parallel
`reversehourglassScore()`	Compute the Reverse Hourglass Score for the Reverse Hourglass Test
`rhScore()`	Compute the Hourglass Score for the Reductive Hourglass Test
`taxid()`	Retrieve taxonomy categories from NCBI Taxonomy
`taxonomy()`	Retrieving Taxonomic Information of a Query Organism
`tf()`	Transform Gene Expression Levels
`tfStability()`	Perform Permutation Tests Under Different Transformations

Reference

All functions