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Phylotranscriptomics Measures

Compute full and partial phylotranscriptomics measures.

TAI()
Compute the Transcriptome Age Index (TAI)
TDI()
Compute the Transcriptome Divergence Index (TDI)
TPI()
Compute the Transcriptome Polymorphism Index (TPI)
TEI()
Compute the Transcriptome Evolutionary Index (TEI)
REMatrix()
Compute a Relative Expression Matrix
RE()
Transform to Relative Expression Levels
pTAI()
Compute the Phylostratum Contribution to the Global Transcriptome Age Index
pTDI()
Compute the Divergence Stratum Contribution to the Global Transcriptome Divergence Index
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
GATAI()
Low level interface function with GATAI

Visualization and Analytics Tools

Visualise phylotranscriptomics patterns

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
PlotSignatureGATAIGeneRemoval()
Plot evolutionary signatures across transcriptomes after GATAI gene removal
PlotSignatureTransformed()
Plot evolutionary signatures across transcriptomes and RNA-seq transformations
PlotVars()
Plot Variance of Expression Profiles
SignatureGATAIGeneRemoval()
Removed genes after GATAI gene removal and plots of evolutionary signatures across transcriptomes before, after GATAI gene removal and with randomly removed genes

A Statistical Framework and Test Statistics

EarlyConservationTest()
Perform Reductive Early Conservation Test
EnrichmentTest()
Phylostratum or Divergence Stratum Enrichment of a given Gene Set based on Fisher's Test
FlatLineTest()
Perform Flat Line Test
LateConservationTest()
Perform Reductive Late Conservation Test
PairwiseTest()
Perform Pairwise Difference Test
ReductiveHourglassTest()
Perform the Reductive Hourglass Test
ReverseHourglassTest()
Perform the Reverse Hourglass Test
bootMatrix()
Compute a Permutation Matrix for Test Statistics
bootTEI()
Compute a Permutation Matrix of Transcriptome Evolutionary Index (TEI)

Differential Gene Expression Analysis

DiffGenes()
Differential Gene Expression Analysis
CollapseReplicates()
Combine Replicates in an ExpressionSet
CombinatorialSignificance()
Compute the Statistical Significance of Each Replicate Combination
Expressed()
Filter for Expressed Genes
SelectGeneSet()
Select a Subset of Genes in an ExpressionSet
PlotReplicateQuality()
Plot the Quality of Biological Replicates
GroupDiffs()
Quantify the significant differences between gene expression distributions of age groups

Taxonomic Information Retrieval

taxid()
Retrieve taxonomy categories from NCBI Taxonomy

Minor Functions for Better Usibility and Additional Analyses

MatchMap()
Match a Phylostratigraphic Map or Divergence Map with a ExpressionMatrix
tf()
Transform Gene Expression Levels
tfStability()
Perform Permutation Tests Under Different Transformations
tfPS()
Transform Phylostratum Values
ecScore()
Compute the Hourglass Score for the EarlyConservationTest
lcScore()
Compute the Hourglass Score for the LateConservationTest
pairScore()
Compute the Pairwise Difference in TAI Score
reversehourglassScore()
Compute the Reverse Hourglass Score for the Reverse Hourglass Test
rhScore()
Compute the Hourglass Score for the Reductive Hourglass Test
age.apply()
Age Category Specific apply Function
geom.mean()
Geometric Mean
harm.mean()
Harmonic Mean
omitMatrix()
Compute TAI or TDI Profiles Omitting a Given Gene
rcpp_boottei_parallel()
rcpp_boottei_parallel
rcpp_pMatrix_parallel()
rcpp_pMatrix_parallel
rcpp_pStrata_parallel()
rcpp_pStrata_parallel
rcpp_tei_parallel()
rcpp_tei_parallel
is_installed_gatai()
Test whether GATAI is installed on user machine

Example Datasets

DivergenceExpressionSetExample
An Example DivergenceExpressionSet Data Set
PhyloExpressionSetExample
An Example PhyloExpressionSet Data Set