Evolutionary Transcriptomics

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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)