R/pTAI.R
pTAI.RdThis function takes a standard ExpressionSet object and computes the partial contribution of the different phylostrata (ps) to the global Transcriptome Age Index profile.
pTAI(ExpressionSet)a standard PhyloExpressionSet object.
This way of computing the partial contribution of the different phylostrata (ps) to the global Transcriptome Age Index profile was introduced by Domazet-Loso and Tautz, 2010. This function (pTAI) computes the partial TAI contribution for each phylostratum and each developmental stage and returns a data matrix storing the partial TAI contribution value for each phylostratum and each developmental stage.
Domazet-Loso T. and Tautz D. (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature (468): 815-818.
pTDI, TAI, TDI, PlotPattern
data(PhyloExpressionSetExample)
# get the partial contribution of phylostrata to the global
# TAI pattern
pTAI(PhyloExpressionSetExample)
#> Zygote Quadrant Globular Heart Torpedo Bent Mature
#> 1 0.3929533 0.3935308 0.4142106 0.4115399 0.4216806 0.4178302 0.3883815
#> 2 0.9521021 0.9547833 0.9748522 0.9674842 0.9632213 0.9285336 0.8661883
#> 3 1.0502814 1.0477016 1.0576104 1.0556300 1.0549156 1.0187303 0.9722031
#> 4 1.3861830 1.3810595 1.3837548 1.3928030 1.3876006 1.3632945 1.3656170
#> 5 1.5527473 1.5489829 1.5360986 1.5500708 1.5468767 1.5531699 1.5769758
#> 6 1.8114772 1.8171167 1.7806803 1.7968463 1.8020203 1.8223456 1.9207232
#> 7 1.8766090 1.8739449 1.8317327 1.8530276 1.8573216 1.8776292 1.9952325
#> 8 1.9417254 1.9357499 1.8877436 1.9089144 1.9117438 1.9478303 2.0778287
#> 9 2.0339192 2.0294517 1.9823091 1.9982678 1.9915249 2.0413791 2.1878074
#> 10 2.4215868 2.4361137 2.3489524 2.3347670 2.3028346 2.3797112 2.5142773
#> 11 2.4900201 2.5079107 2.4104647 2.3980760 2.3651571 2.4422093 2.5961316
#> 12 3.2299418 3.2256139 3.1071348 3.1166934 3.0739935 3.1765113 3.3903336