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This function takes a standard ExpressionSet object and computes the partial contribution of the different phylostrata (ps) to the global Transcriptome Age Index profile.

Usage

pTAI(ExpressionSet)

Arguments

ExpressionSet

a standard PhyloExpressionSet object.

Details

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.

References

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

See also

Author

Hajk-Georg Drost

Examples


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