A Framework to Perform Phylotranscriptomics Analyses for Evolutionary Developmental Biology Research

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Documentation for package ‘myTAI’ version 0.0.2

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age.apply Age class specific apply function
bar.colors Color palette for barplots
bootMatrix Compute a permutation matrix for test statistics
combinatorialSignificance Compute the statistical significance of each replicate combination
DivergenceExpressionSetExample A standard DivergenceExpressionSet example
EarlyConservationTest Perform the Reductive Early Conservation Test
ecScore Compute the Hourglass Score for the EarlyConservationTest
FlatLineTest Perform the Flat Line Test
is.ExpressionSet Testing the validaty of a PhyloExpressionSet or DivergenceExpressionSet standard
MatchMap Match a Phylostratigraphic Map or Divergence Map with a ExpressionMatrix
omitMatrix Compute TAI or TDI profiles omitting a given gene
PhyloExpressionSetExample A standard PhyloExpressionSet example
PlotBarRE Plot the mean relative expression levels as barplot
PlotCorrelation Plot the correlation between Phylostrata and Divergence-Strata of a given PhyloExpressionSet and DivergenceExpressionSet
PlotDistribution Plot the frequency distribution of Phylostrata or Divergence-Strata
PlotMeans Plot the Mean Expression Profiles of Phylostrata or Divergence-Strata
PlotPattern Plot the Transcriptome Age Index or Transcriptome Divergence Index
PlotRE Plot relative expression levels
pMatrix Compute the partial TAI or TDI values for each single gene in a standard PhyloExpressionSet or DivergenceExpressionSet object
RE Transform to relative expression levels
ReductiveHourglassTest Perform the Reductive Hourglass Test
REMatrix Compute relative expression profiles for Phylostrata or Divergence-Strata available in a PhyloExpressionSet or DivergenceExpressionSet
rhScore Compute the Hourglass Score for the Reductive Hourglass Test
TAI Compute the Transcriptome Age Index (TAI)
TDI Compute the Transcriptome Divergence Index (TDI)
tf Transform the gene expression set of a given PhyloExpressionSet or DivergenceExpressionSet