# Evolutionary Transcriptomics

## Documentation for package ‘myTAI’ version 0.9.3

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

## Help Pages

age.apply | Age Category Specific apply Function
bar.colors | Color palette for barplots
bootMatrix | Compute a Permutation Matrix for Test Statistics
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
ecScore | Compute the Hourglass Score for the EarlyConservationTest
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
geom.mean | Geometric Mean
GroupDiffs | Quantify the significant differences between gene expression distributions of age groups
harm.mean | Harmonic Mean
is.ExpressionSet | Test ExpressionSet Standard
MatchMap | Match a Phylostratigraphic Map or Divergence Map with a ExpressionMatrix
omitMatrix | Compute TAI or TDI Profiles Omitting a Given Gene
PhyloExpressionSetExample | An Example PhyloExpressionSet Data Set
PlotBarRE | Plot Mean Relative Expression Levels as Barplot
PlotCategoryExpr | Plot the Expression Levels of each Age or Divergence Category as Boxplot, Violinplot, or Dotplot
PlotCIRatio | Plot Transcriptome Index using bootstrapping and confidence intervals
PlotContribution | Plot Cumuative 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
PlotVars | Plot Variance of Expression Profiles
pMatrix | Compute Partial TAI or TDI Values
pStrata | Compute Partial 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
RE | Transform to Relative Expression Levels
ReductiveHourglassTest | Perform the Reductive Hourglass Test
REMatrix | Compute a Relative Expression Matrix
reversehourglassScore | Compute the Reverse Hourglass Score for the Reverse Hourglass Test
ReverseHourglassTest | Perform the Reverse Hourglass Test
rhScore | Compute the Hourglass Score for the Reductive Hourglass Test
SelectGeneSet | Select a Subset of Genes in an ExpressionSet
TAI | Compute the Transcriptome Age Index (TAI)
taxid | Retrieve taxonomy categories from NCBI Taxonomy
taxonomy | Retrieving Taxonomic Information of a Query Organism
TDI | Compute the Transcriptome Divergence Index (TDI)
tf | Transform Gene Expression Levels
TPI | Compute the Transcriptome Polymorphism Index (TPI)