Compute the Divergence Stratum Contribution to the Global Transcriptome Divergence Index

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.

Usage

pTDI(ExpressionSet)

Arguments

ExpressionSet: a standard DivergenceExpressionSet object.

Details

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.

References

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.

Author

Hajk-Georg Drost

Examples


data(DivergenceExpressionSetExample)

# get the partial contribution of divergence strata to the global
# TDI pattern
pTAI(DivergenceExpressionSetExample)
#>       Zygote  Quadrant  Globular     Heart   Torpedo      Bent    Mature
#> 1  0.2174378 0.2207644 0.2309211 0.2214881 0.2195601 0.2047938 0.1704023
#> 2  0.4800055 0.4762352 0.4821244 0.4752145 0.4799418 0.4695871 0.4288670
#> 3  0.7742988 0.7597816 0.7797646 0.7826244 0.8033702 0.8034316 0.7769026
#> 4  1.1463780 1.1285545 1.1408903 1.1528497 1.1694967 1.1784113 1.1933157
#> 5  1.5652686 1.5489672 1.5545589 1.5698173 1.5934158 1.6003011 1.6330444
#> 6  2.0899161 2.0609661 2.0666314 2.1015199 2.1163138 2.1306059 2.1932280
#> 7  2.6262330 2.6035894 2.6012719 2.6453427 2.6477490 2.6664143 2.8085434
#> 8  3.2211299 3.1990804 3.1767694 3.2319604 3.2292835 3.2693046 3.4412353
#> 9  3.8396769 3.8299654 3.7793476 3.8353941 3.8272391 3.8971210 4.0753877
#> 10 4.5320286 4.5632002 4.4857052 4.5008685 4.4664774 4.5307040 4.6902921