Man pages for drostlab/myTAI
Evolutionary Transcriptomics
| 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... |
| CollapseReplicates | Combine Replicates in an ExpressionSet |
| CombinatorialSignificance | Compute the Statistical Significance of Each Replicate... |
| 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... |
| Expressed | Filter for Expressed Genes |
| FlatLineTest | Perform Flat Line Test |
| GATAI | Low level interface function with GATAI |
| geom.mean | Geometric Mean |
| GroupDiffs | Quantify the significant differences between gene expression... |
| harm.mean | Harmonic Mean |
| is.ExpressionSet | Test ExpressionSet Standard |
| is_installed_gatai | Test whether GATAI is installed on user machine |
| LateConservationTest | Perform Reductive Late Conservation Test |
| lcScore | Compute the Hourglass Score for the LateConservationTest |
| MatchMap | Match a Phylostratigraphic Map or Divergence Map with a... |
| omitMatrix | Compute TAI or TDI Profiles Omitting a Given Gene |
| pairScore | Compute the Pairwise Difference in TAI Score |
| PairwiseTest | Perform Pairwise Difference Test |
| 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... |
| PlotCIRatio | Plot Transcriptome Index using bootstrapping and confidence... |
| PlotContribution | Plot Cumulative Transcriptome Index |
| PlotCorrelation | Plot the Correlation Between Phylostrata and Divergence... |
| PlotDistribution | Plot the Frequency Distribution of Phylostrata or Divergence... |
| plot_distribution_expression | Comparing expression levels distributions across stages |
| plot_distribution_expression_partialTAI | Comparing expression/partial TAI distributions across the... |
| plot_distribution_partialTAI | Comparing partial TAI distributions across stages |
| plot_distribution_partialTAI_qqplot | QQ plot comparing partial TAI distributions across... |
| PlotEnrichment | Plot the Phylostratum or Divergence Stratum Enrichment of a... |
| plot_gene_set | Plot the Expression Profiles of a Gene Set |
| plot_gene_set_mean | Plot the Mean Gene Expression Profiles with Optional Standard... |
| PlotGroupDiffs | Plot the significant differences between gene expression... |
| PlotMeans | Plot Mean Expression Profiles |
| PlotMedians | Plot Median Expression Profiles |
| PlotPattern | Plot the Transcriptome Age Index or Transcriptome Divergence... |
| 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... |
| PlotSignatureGeneQuantiles | Plot evolutionary signatures across transcriptomes, removing... |
| PlotSignatureMultiple | Plot evolutionary signatures across transcriptomes, for... |
| PlotSignatureTransformed | Plot evolutionary signatures across transcriptomes and... |
| PlotVars | Plot Variance of Expression Profiles |
| 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... |
| pTAI | Compute the Phylostratum Contribution to the Global... |
| pTDI | Compute the Divergence Stratum Contribution to the Global... |
| rcpp_boottei_parallel | rcpp_boottei_parallel |
| rcpp_pMatrix_parallel | rcpp_pMatrix_parallel |
| rcpp_pStrata_parallel | rcpp_pStrata_parallel |
| rcpp_tei_parallel | rcpp_tei_parallel |
| 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... |
| 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 |
| SignatureGATAIGeneRemoval | Removed genes after GATAI gene removal and plots of... |
| TAI | Compute the Transcriptome Age Index (TAI) |
| taxid | Retrieve taxonomy categories from NCBI Taxonomy |
| TDI | Compute the Transcriptome Divergence Index (TDI) |
| TEI | Compute the Transcriptome Evolutionary Index (TEI) |
| tf | Transform Gene Expression Levels |
| tfPS | Transform Phylostratum Values |
| tfStability | Perform Permutation Tests Under Different Transformations |
| TopExpressionGenes | Top quantile expression genes |
| TopVarianceGenes | Top quantile expression-variance genes |
| TPI | Compute the Transcriptome Polymorphism Index (TPI) |
