pTDI: Compute the Divergence Stratum Contribution to the Global...
In myTAI: Evolutionary Transcriptomics

Description Usage Arguments Details Author(s) References See Also Examples

This function takes a standard ExpressionSet object and computes the partial contribution of the different divergence strata (ds) to the global Transcriptome Divergence Index profile.

1	pTDI(ExpressionSet)

ExpressionSet

a standard DivergenceExpressionSet object.

This function (pTDI) computes the partial TDI contribution for each phylostratum and each developmental stage and returns a data matrix storing the partial TDI contribution value for each divergence and each developmental stage.

Hajk-Georg Drost

Domazet-Loso T. and Tautz D. (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature (468): 815-818.

Quint M et al. (2012). A transcriptomic hourglass in plant embryogenesis. Nature (490): 98-101.

Drost HG et al. (2015). Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis. Mol Biol Evol. 32 (5): 1221-1231 doi:10.1093/molbev/msv012.

pTAI, TAI, TDI, PlotPattern

data(DivergenceExpressionSetExample)

# get the partial contribution of divergence strata to the global
# TDI pattern
pTAI(DivergenceExpressionSetExample)