Package index • myTAI

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

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

PlotSignatureGeneQuantiles(): Plot evolutionary signatures across transcriptomes, removing top level genes

PlotSignatureMultiple(): Plot evolutionary signatures across transcriptomes, for multiple expression sets

PlotSignatureTransformed(): Plot evolutionary signatures across transcriptomes and RNA-seq transformations

PlotVars(): Plot Variance of Expression Profiles

plot_distribution_expression(): Comparing expression levels distributions across stages

plot_distribution_expression_partialTAI(): Comparing expression/partial TAI distributions across the different developmental stages

plot_distribution_partialTAI(): Comparing partial TAI distributions across stages

plot_distribution_partialTAI_qqplot(): QQ plot comparing partial TAI distributions across developmental stages against a reference stage

plot_gene_set(): Plot the Expression Profiles of a Gene Set

plot_gene_set_mean(): Plot the Mean Gene Expression Profiles with Optional Standard Deviation and Labels

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

TopExpressionGenes(): Top quantile expression genes

TopVarianceGenes(): Top quantile expression-variance genes

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

plot_gene_set_mean(): Plot the Mean Gene Expression Profiles with Optional Standard Deviation and Labels

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